Multiple sequence alignment - TraesCS2D01G452500

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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 TraesCS2D01G452500 chr2D 100.000 2537 0 0 1 2537 561932585 561930049 0.000000e+00 4686.0
1 TraesCS2D01G452500 chr2D 78.443 501 92 14 1041 1536 560561891 560562380 1.890000e-81 313.0
2 TraesCS2D01G452500 chr2B 92.205 1719 62 22 498 2162 671211258 671209558 0.000000e+00 2366.0
3 TraesCS2D01G452500 chr2B 74.744 293 65 6 1128 1417 707982401 707982687 3.430000e-24 122.0
4 TraesCS2D01G452500 chr2A 93.078 1098 37 14 497 1586 702191090 702190024 0.000000e+00 1570.0
5 TraesCS2D01G452500 chr2A 88.277 563 15 16 1608 2162 702189757 702189238 5.960000e-176 627.0
6 TraesCS2D01G452500 chr2A 86.902 481 22 18 22 496 736471653 736472098 3.770000e-138 501.0
7 TraesCS2D01G452500 chr2A 78.740 508 91 15 1034 1536 702243116 702242621 8.750000e-85 324.0
8 TraesCS2D01G452500 chr2A 96.923 65 2 0 2229 2293 702189223 702189159 2.670000e-20 110.0
9 TraesCS2D01G452500 chr5D 96.393 499 12 3 1 497 426788074 426787580 0.000000e+00 817.0
10 TraesCS2D01G452500 chr5D 78.344 157 25 7 2386 2537 56807292 56807140 2.690000e-15 93.5
11 TraesCS2D01G452500 chr7B 90.164 488 22 6 20 497 746927984 746927513 1.670000e-171 612.0
12 TraesCS2D01G452500 chr7B 85.714 63 8 1 2446 2508 524395652 524395591 5.860000e-07 65.8
13 TraesCS2D01G452500 chr3A 86.538 520 30 14 1 497 705932450 705932952 1.030000e-148 536.0
14 TraesCS2D01G452500 chr3A 90.127 314 14 10 204 514 738142315 738142016 2.370000e-105 392.0
15 TraesCS2D01G452500 chr3A 91.026 156 5 4 1 151 738144372 738144221 4.280000e-48 202.0
16 TraesCS2D01G452500 chr3A 94.340 53 0 1 113 165 705932632 705932681 7.520000e-11 78.7
17 TraesCS2D01G452500 chr4D 86.614 127 15 2 369 494 45635163 45635288 3.400000e-29 139.0
18 TraesCS2D01G452500 chr7D 81.967 122 19 3 373 493 51745903 51745784 1.610000e-17 100.0
19 TraesCS2D01G452500 chr5B 82.243 107 14 5 2379 2484 519441894 519441792 1.250000e-13 87.9
20 TraesCS2D01G452500 chr6D 82.927 82 14 0 1128 1209 25952836 25952917 9.730000e-10 75.0


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 TraesCS2D01G452500 chr2D 561930049 561932585 2536 True 4686.00 4686 100.000000 1 2537 1 chr2D.!!$R1 2536
1 TraesCS2D01G452500 chr2B 671209558 671211258 1700 True 2366.00 2366 92.205000 498 2162 1 chr2B.!!$R1 1664
2 TraesCS2D01G452500 chr2A 702189159 702191090 1931 True 769.00 1570 92.759333 497 2293 3 chr2A.!!$R2 1796
3 TraesCS2D01G452500 chr3A 705932450 705932952 502 False 307.35 536 90.439000 1 497 2 chr3A.!!$F1 496
4 TraesCS2D01G452500 chr3A 738142016 738144372 2356 True 297.00 392 90.576500 1 514 2 chr3A.!!$R1 513

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
820 1623 0.249447 CGCAGTCACTGAACTCCACA 60.249 55.0 9.7 0.0 32.44 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 3423 0.035056 AAGTCTGCATCTTTCCCCCG 60.035 55.0 0.0 0.0 0.0 5.73 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
29 30 2.260844 ATGGAGAGAGAGAGAGAGCG 57.739 55.000 0.00 0.00 0.00 5.03
30 31 0.463654 TGGAGAGAGAGAGAGAGCGC 60.464 60.000 0.00 0.00 0.00 5.92
31 32 1.498865 GGAGAGAGAGAGAGAGCGCG 61.499 65.000 0.00 0.00 0.00 6.86
32 33 2.105960 GAGAGAGAGAGAGAGCGCGC 62.106 65.000 26.66 26.66 0.00 6.86
55 56 5.810074 GCCTATGAGAGAGAACTTCACTTTC 59.190 44.000 1.24 1.24 0.00 2.62
98 101 5.850046 AAAAATGGAGAGAGGGAGAGAAA 57.150 39.130 0.00 0.00 0.00 2.52
99 102 5.434182 AAAATGGAGAGAGGGAGAGAAAG 57.566 43.478 0.00 0.00 0.00 2.62
171 214 2.373540 AAAAGTAGTATGACGCGCCA 57.626 45.000 5.73 0.00 0.00 5.69
172 215 1.922570 AAAGTAGTATGACGCGCCAG 58.077 50.000 5.73 0.00 0.00 4.85
173 216 1.100510 AAGTAGTATGACGCGCCAGA 58.899 50.000 5.73 0.00 0.00 3.86
175 218 1.065701 AGTAGTATGACGCGCCAGAAG 59.934 52.381 5.73 0.00 0.00 2.85
179 222 2.016393 TATGACGCGCCAGAAGGAGG 62.016 60.000 5.73 0.00 36.89 4.30
180 223 3.760035 GACGCGCCAGAAGGAGGA 61.760 66.667 5.73 0.00 36.89 3.71
184 227 1.234615 CGCGCCAGAAGGAGGAAAAA 61.235 55.000 0.00 0.00 36.89 1.94
185 228 0.523519 GCGCCAGAAGGAGGAAAAAG 59.476 55.000 0.00 0.00 36.89 2.27
186 229 1.168714 CGCCAGAAGGAGGAAAAAGG 58.831 55.000 0.00 0.00 36.89 3.11
187 230 1.271379 CGCCAGAAGGAGGAAAAAGGA 60.271 52.381 0.00 0.00 36.89 3.36
189 232 2.822561 GCCAGAAGGAGGAAAAAGGAAG 59.177 50.000 0.00 0.00 36.89 3.46
192 235 4.764308 CCAGAAGGAGGAAAAAGGAAGAAG 59.236 45.833 0.00 0.00 36.89 2.85
193 236 5.380900 CAGAAGGAGGAAAAAGGAAGAAGT 58.619 41.667 0.00 0.00 0.00 3.01
194 237 6.465894 CCAGAAGGAGGAAAAAGGAAGAAGTA 60.466 42.308 0.00 0.00 36.89 2.24
195 238 6.998673 CAGAAGGAGGAAAAAGGAAGAAGTAA 59.001 38.462 0.00 0.00 0.00 2.24
197 240 6.517013 AGGAGGAAAAAGGAAGAAGTAAGT 57.483 37.500 0.00 0.00 0.00 2.24
198 241 6.299922 AGGAGGAAAAAGGAAGAAGTAAGTG 58.700 40.000 0.00 0.00 0.00 3.16
199 242 6.101296 AGGAGGAAAAAGGAAGAAGTAAGTGA 59.899 38.462 0.00 0.00 0.00 3.41
202 245 6.773200 AGGAAAAAGGAAGAAGTAAGTGAAGG 59.227 38.462 0.00 0.00 0.00 3.46
326 370 4.015406 CAGGCCTACCACCGTGCA 62.015 66.667 3.98 0.00 39.06 4.57
346 390 3.628017 CACGGTTTTACCTCTGCAAAAG 58.372 45.455 0.00 0.00 35.66 2.27
365 409 0.321671 GCCTACTCTGCCTCACACAA 59.678 55.000 0.00 0.00 0.00 3.33
371 415 0.685097 TCTGCCTCACACAACCTACC 59.315 55.000 0.00 0.00 0.00 3.18
380 424 4.980573 TCACACAACCTACCTGCTTAATT 58.019 39.130 0.00 0.00 0.00 1.40
399 443 3.630892 TTAAACCTGCCACCGCTAATA 57.369 42.857 0.00 0.00 35.36 0.98
400 444 2.500392 AAACCTGCCACCGCTAATAA 57.500 45.000 0.00 0.00 35.36 1.40
409 453 0.810031 ACCGCTAATAACCTGCTGCG 60.810 55.000 0.00 0.00 42.52 5.18
441 485 3.821033 ACTGCACGAATCTTAAAAAGGCT 59.179 39.130 0.00 0.00 0.00 4.58
534 586 9.436957 CTCAATTTCAGAAAAAGCTAGGTAGTA 57.563 33.333 0.00 0.00 0.00 1.82
615 667 8.586570 TGTTAATGTTGCAGTTAAGATTTTGG 57.413 30.769 0.00 0.00 0.00 3.28
820 1623 0.249447 CGCAGTCACTGAACTCCACA 60.249 55.000 9.70 0.00 32.44 4.17
822 1625 1.599542 GCAGTCACTGAACTCCACAAC 59.400 52.381 9.70 0.00 32.44 3.32
898 1701 2.489329 AGACGCCACCTGAATTTCATTG 59.511 45.455 0.00 0.89 0.00 2.82
912 1715 0.767375 TCATTGCCTAGCAGGATCCC 59.233 55.000 8.55 0.00 40.61 3.85
1004 1821 2.422276 AAAACCAGCGCAAAGATGAC 57.578 45.000 11.47 0.00 38.85 3.06
1024 1841 1.003233 AGGCCTTCGCAAGTTCTCC 60.003 57.895 0.00 0.00 36.38 3.71
1127 2005 2.383527 CGAGCAACAAGGACCTCGC 61.384 63.158 0.00 0.00 40.35 5.03
1503 2465 4.608948 CTCCAAGTTCAGTAAGGAGTGT 57.391 45.455 0.00 0.00 40.71 3.55
1676 2907 2.727777 CCATCAAAGCGAATGCATGAG 58.272 47.619 0.00 0.00 46.23 2.90
1700 2931 1.921887 CCATCGTGCATCAATGTTTGC 59.078 47.619 0.00 4.47 39.33 3.68
1836 3067 5.292589 CCATTTGTTGATTAGCAAGGCAATC 59.707 40.000 0.00 0.00 37.12 2.67
1837 3068 3.763097 TGTTGATTAGCAAGGCAATCG 57.237 42.857 0.00 0.00 37.12 3.34
2012 3250 1.552799 ATGGGTCATGCTGTGTCCGA 61.553 55.000 0.00 0.00 36.95 4.55
2080 3321 2.819595 CCACGAAGGCCATGTCCG 60.820 66.667 5.01 2.90 0.00 4.79
2162 3407 4.168922 TCGAGTCGAAGATGCAAACTTA 57.831 40.909 13.98 0.00 40.67 2.24
2163 3408 4.744570 TCGAGTCGAAGATGCAAACTTAT 58.255 39.130 13.98 0.00 40.67 1.73
2164 3409 5.168569 TCGAGTCGAAGATGCAAACTTATT 58.831 37.500 13.98 0.00 40.67 1.40
2165 3410 5.637810 TCGAGTCGAAGATGCAAACTTATTT 59.362 36.000 13.98 0.00 40.67 1.40
2166 3411 6.147164 TCGAGTCGAAGATGCAAACTTATTTT 59.853 34.615 13.98 0.00 40.67 1.82
2167 3412 6.797033 CGAGTCGAAGATGCAAACTTATTTTT 59.203 34.615 6.73 0.00 40.67 1.94
2168 3413 7.955324 CGAGTCGAAGATGCAAACTTATTTTTA 59.045 33.333 6.73 0.00 40.67 1.52
2169 3414 9.774742 GAGTCGAAGATGCAAACTTATTTTTAT 57.225 29.630 9.02 0.00 40.67 1.40
2191 3436 0.320050 TTTTTGCGGGGGAAAGATGC 59.680 50.000 0.00 0.00 0.00 3.91
2192 3437 0.829602 TTTTGCGGGGGAAAGATGCA 60.830 50.000 0.00 0.00 0.00 3.96
2193 3438 1.250154 TTTGCGGGGGAAAGATGCAG 61.250 55.000 0.00 0.00 36.83 4.41
2194 3439 2.135903 TTGCGGGGGAAAGATGCAGA 62.136 55.000 0.00 0.00 36.83 4.26
2195 3440 2.115291 GCGGGGGAAAGATGCAGAC 61.115 63.158 0.00 0.00 0.00 3.51
2196 3441 1.604378 CGGGGGAAAGATGCAGACT 59.396 57.895 0.00 0.00 0.00 3.24
2197 3442 0.035056 CGGGGGAAAGATGCAGACTT 60.035 55.000 0.00 0.00 0.00 3.01
2198 3443 1.756430 GGGGGAAAGATGCAGACTTC 58.244 55.000 8.93 3.27 0.00 3.01
2211 3456 1.885887 CAGACTTCGGAAAATTGGCCA 59.114 47.619 0.00 0.00 0.00 5.36
2212 3457 1.886542 AGACTTCGGAAAATTGGCCAC 59.113 47.619 3.88 0.00 0.00 5.01
2213 3458 0.596082 ACTTCGGAAAATTGGCCACG 59.404 50.000 3.88 4.51 0.00 4.94
2214 3459 0.878416 CTTCGGAAAATTGGCCACGA 59.122 50.000 3.88 7.50 0.00 4.35
2215 3460 1.472480 CTTCGGAAAATTGGCCACGAT 59.528 47.619 3.88 0.00 0.00 3.73
2216 3461 0.808125 TCGGAAAATTGGCCACGATG 59.192 50.000 3.88 0.00 0.00 3.84
2217 3462 0.808125 CGGAAAATTGGCCACGATGA 59.192 50.000 3.88 0.00 0.00 2.92
2218 3463 1.405105 CGGAAAATTGGCCACGATGAT 59.595 47.619 3.88 0.00 0.00 2.45
2219 3464 2.159254 CGGAAAATTGGCCACGATGATT 60.159 45.455 3.88 0.00 0.00 2.57
2220 3465 3.447742 GGAAAATTGGCCACGATGATTC 58.552 45.455 3.88 6.32 0.00 2.52
2221 3466 3.131046 GGAAAATTGGCCACGATGATTCT 59.869 43.478 3.88 0.00 0.00 2.40
2222 3467 4.338118 GGAAAATTGGCCACGATGATTCTA 59.662 41.667 3.88 0.00 0.00 2.10
2223 3468 5.163561 GGAAAATTGGCCACGATGATTCTAA 60.164 40.000 3.88 0.00 0.00 2.10
2224 3469 5.505173 AAATTGGCCACGATGATTCTAAG 57.495 39.130 3.88 0.00 0.00 2.18
2225 3470 1.953559 TGGCCACGATGATTCTAAGC 58.046 50.000 0.00 0.00 0.00 3.09
2226 3471 1.486310 TGGCCACGATGATTCTAAGCT 59.514 47.619 0.00 0.00 0.00 3.74
2227 3472 2.092968 TGGCCACGATGATTCTAAGCTT 60.093 45.455 0.00 3.48 0.00 3.74
2257 3502 4.083565 TCCTAAATTTTACTGTGTGGGCC 58.916 43.478 0.00 0.00 0.00 5.80
2286 3531 5.878406 TTTCCAACCAAATGTTACCATGT 57.122 34.783 0.00 0.00 34.69 3.21
2293 3538 5.887754 ACCAAATGTTACCATGTACTTCCT 58.112 37.500 0.00 0.00 0.00 3.36
2294 3539 5.710099 ACCAAATGTTACCATGTACTTCCTG 59.290 40.000 0.00 0.00 0.00 3.86
2295 3540 5.710099 CCAAATGTTACCATGTACTTCCTGT 59.290 40.000 0.00 0.00 0.00 4.00
2296 3541 6.208599 CCAAATGTTACCATGTACTTCCTGTT 59.791 38.462 0.00 0.00 0.00 3.16
2297 3542 7.255801 CCAAATGTTACCATGTACTTCCTGTTT 60.256 37.037 0.00 0.00 0.00 2.83
2298 3543 8.788806 CAAATGTTACCATGTACTTCCTGTTTA 58.211 33.333 0.00 0.00 0.00 2.01
2299 3544 8.927675 AATGTTACCATGTACTTCCTGTTTAA 57.072 30.769 0.00 0.00 0.00 1.52
2300 3545 8.927675 ATGTTACCATGTACTTCCTGTTTAAA 57.072 30.769 0.00 0.00 0.00 1.52
2301 3546 8.385898 TGTTACCATGTACTTCCTGTTTAAAG 57.614 34.615 0.00 0.00 0.00 1.85
2302 3547 8.212312 TGTTACCATGTACTTCCTGTTTAAAGA 58.788 33.333 0.00 0.00 0.00 2.52
2303 3548 9.227777 GTTACCATGTACTTCCTGTTTAAAGAT 57.772 33.333 0.00 0.00 0.00 2.40
2427 3672 8.812513 TCAATCTATTCATCAAACATCAAGGT 57.187 30.769 0.00 0.00 0.00 3.50
2428 3673 9.904198 TCAATCTATTCATCAAACATCAAGGTA 57.096 29.630 0.00 0.00 0.00 3.08
2432 3677 9.817809 TCTATTCATCAAACATCAAGGTAGTAC 57.182 33.333 0.00 0.00 0.00 2.73
2433 3678 9.599866 CTATTCATCAAACATCAAGGTAGTACA 57.400 33.333 2.06 0.00 0.00 2.90
2434 3679 8.862325 ATTCATCAAACATCAAGGTAGTACAA 57.138 30.769 2.06 0.00 0.00 2.41
2436 3681 8.684386 TCATCAAACATCAAGGTAGTACAAAA 57.316 30.769 2.06 0.00 0.00 2.44
2437 3682 9.126151 TCATCAAACATCAAGGTAGTACAAAAA 57.874 29.630 2.06 0.00 0.00 1.94
2438 3683 9.180678 CATCAAACATCAAGGTAGTACAAAAAC 57.819 33.333 2.06 0.00 0.00 2.43
2440 3685 8.908903 TCAAACATCAAGGTAGTACAAAAACAT 58.091 29.630 2.06 0.00 0.00 2.71
2441 3686 9.180678 CAAACATCAAGGTAGTACAAAAACATC 57.819 33.333 2.06 0.00 0.00 3.06
2442 3687 8.458573 AACATCAAGGTAGTACAAAAACATCA 57.541 30.769 2.06 0.00 0.00 3.07
2444 3689 7.936847 ACATCAAGGTAGTACAAAAACATCAGA 59.063 33.333 2.06 0.00 0.00 3.27
2445 3690 8.783093 CATCAAGGTAGTACAAAAACATCAGAA 58.217 33.333 2.06 0.00 0.00 3.02
2446 3691 8.740123 TCAAGGTAGTACAAAAACATCAGAAA 57.260 30.769 2.06 0.00 0.00 2.52
2448 3693 8.402472 CAAGGTAGTACAAAAACATCAGAAACA 58.598 33.333 2.06 0.00 0.00 2.83
2450 3695 8.403236 AGGTAGTACAAAAACATCAGAAACAAC 58.597 33.333 2.06 0.00 0.00 3.32
2451 3696 8.185505 GGTAGTACAAAAACATCAGAAACAACA 58.814 33.333 2.06 0.00 0.00 3.33
2452 3697 9.562583 GTAGTACAAAAACATCAGAAACAACAA 57.437 29.630 0.00 0.00 0.00 2.83
2463 3708 9.260002 ACATCAGAAACAACAAAAATTACATCC 57.740 29.630 0.00 0.00 0.00 3.51
2464 3709 9.258826 CATCAGAAACAACAAAAATTACATCCA 57.741 29.630 0.00 0.00 0.00 3.41
2467 3712 9.044150 CAGAAACAACAAAAATTACATCCATGT 57.956 29.630 0.00 0.00 44.48 3.21
2471 3716 9.995003 AACAACAAAAATTACATCCATGTATGT 57.005 25.926 9.07 9.07 42.32 2.29
2478 3723 3.492102 ACATCCATGTATGTAGGCCAC 57.508 47.619 5.01 1.31 38.31 5.01
2479 3724 2.106511 ACATCCATGTATGTAGGCCACC 59.893 50.000 5.01 0.00 38.31 4.61
2480 3725 2.190398 TCCATGTATGTAGGCCACCT 57.810 50.000 5.01 0.00 37.71 4.00
2481 3726 3.338110 TCCATGTATGTAGGCCACCTA 57.662 47.619 5.01 0.00 34.61 3.08
2484 3729 2.168458 TGTATGTAGGCCACCTAGCA 57.832 50.000 5.01 0.00 36.71 3.49
2485 3730 2.473070 TGTATGTAGGCCACCTAGCAA 58.527 47.619 5.01 0.00 36.71 3.91
2486 3731 2.169769 TGTATGTAGGCCACCTAGCAAC 59.830 50.000 5.01 0.00 36.71 4.17
2487 3732 1.285280 ATGTAGGCCACCTAGCAACA 58.715 50.000 5.01 0.00 36.71 3.33
2488 3733 1.060729 TGTAGGCCACCTAGCAACAA 58.939 50.000 5.01 0.00 36.71 2.83
2490 3735 2.041081 TGTAGGCCACCTAGCAACAATT 59.959 45.455 5.01 0.00 36.71 2.32
2492 3737 2.723273 AGGCCACCTAGCAACAATTAC 58.277 47.619 5.01 0.00 28.47 1.89
2493 3738 2.041081 AGGCCACCTAGCAACAATTACA 59.959 45.455 5.01 0.00 28.47 2.41
2494 3739 2.823154 GGCCACCTAGCAACAATTACAA 59.177 45.455 0.00 0.00 0.00 2.41
2495 3740 3.119495 GGCCACCTAGCAACAATTACAAG 60.119 47.826 0.00 0.00 0.00 3.16
2497 3742 3.505680 CCACCTAGCAACAATTACAAGCA 59.494 43.478 0.00 0.00 0.00 3.91
2498 3743 4.158394 CCACCTAGCAACAATTACAAGCAT 59.842 41.667 0.00 0.00 0.00 3.79
2499 3744 5.336690 CCACCTAGCAACAATTACAAGCATT 60.337 40.000 0.00 0.00 0.00 3.56
2509 3754 3.900855 CAAGCATTGGAGCGAGCT 58.099 55.556 0.00 0.00 43.94 4.09
2510 3755 1.428219 CAAGCATTGGAGCGAGCTG 59.572 57.895 0.84 0.00 43.94 4.24
2511 3756 1.022982 CAAGCATTGGAGCGAGCTGA 61.023 55.000 0.84 0.00 43.94 4.26
2512 3757 0.321919 AAGCATTGGAGCGAGCTGAA 60.322 50.000 0.84 0.00 40.15 3.02
2514 3759 1.720301 CATTGGAGCGAGCTGAAGC 59.280 57.895 0.84 0.00 42.49 3.86
2515 3760 1.451028 ATTGGAGCGAGCTGAAGCC 60.451 57.895 0.84 0.00 43.38 4.35
2523 3768 4.421515 AGCTGAAGCCGCTGCCAT 62.422 61.111 0.00 0.00 43.38 4.40
2525 3770 2.437180 CTGAAGCCGCTGCCATCA 60.437 61.111 0.00 1.24 38.69 3.07
2527 3772 0.533531 CTGAAGCCGCTGCCATCATA 60.534 55.000 6.66 0.00 38.69 2.15
2528 3773 0.533531 TGAAGCCGCTGCCATCATAG 60.534 55.000 0.00 0.00 38.69 2.23
2530 3775 3.360340 GCCGCTGCCATCATAGCC 61.360 66.667 0.00 0.00 36.60 3.93
2531 3776 2.670934 CCGCTGCCATCATAGCCC 60.671 66.667 0.00 0.00 36.60 5.19
2532 3777 2.670934 CGCTGCCATCATAGCCCC 60.671 66.667 0.00 0.00 36.60 5.80
2533 3778 2.842058 GCTGCCATCATAGCCCCT 59.158 61.111 0.00 0.00 33.89 4.79
2535 3780 1.377994 CTGCCATCATAGCCCCTCC 59.622 63.158 0.00 0.00 0.00 4.30
2536 3781 2.134630 CTGCCATCATAGCCCCTCCC 62.135 65.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.099921 TGAAGTTCTCTCTCATAGGCGC 59.900 50.000 0.00 0.00 0.00 6.53
30 31 3.380004 AGTGAAGTTCTCTCTCATAGGCG 59.620 47.826 4.17 0.00 0.00 5.52
31 32 5.337578 AAGTGAAGTTCTCTCTCATAGGC 57.662 43.478 7.86 0.00 0.00 3.93
32 33 7.169158 AGAAAGTGAAGTTCTCTCTCATAGG 57.831 40.000 10.14 0.00 29.04 2.57
98 101 3.498397 CCAACGTTTATCTGTCACAAGCT 59.502 43.478 0.00 0.00 0.00 3.74
99 102 3.496884 TCCAACGTTTATCTGTCACAAGC 59.503 43.478 0.00 0.00 0.00 4.01
154 197 1.100510 TCTGGCGCGTCATACTACTT 58.899 50.000 16.48 0.00 0.00 2.24
155 198 1.065701 CTTCTGGCGCGTCATACTACT 59.934 52.381 16.48 0.00 0.00 2.57
157 200 0.384309 CCTTCTGGCGCGTCATACTA 59.616 55.000 16.48 0.00 0.00 1.82
161 204 2.185350 CTCCTTCTGGCGCGTCAT 59.815 61.111 16.48 0.00 0.00 3.06
163 206 2.781595 TTTCCTCCTTCTGGCGCGTC 62.782 60.000 2.29 2.29 0.00 5.19
164 207 2.391724 TTTTCCTCCTTCTGGCGCGT 62.392 55.000 8.43 0.00 0.00 6.01
165 208 1.234615 TTTTTCCTCCTTCTGGCGCG 61.235 55.000 0.00 0.00 0.00 6.86
166 209 0.523519 CTTTTTCCTCCTTCTGGCGC 59.476 55.000 0.00 0.00 0.00 6.53
167 210 1.168714 CCTTTTTCCTCCTTCTGGCG 58.831 55.000 0.00 0.00 0.00 5.69
168 211 2.586648 TCCTTTTTCCTCCTTCTGGC 57.413 50.000 0.00 0.00 0.00 4.85
170 213 5.380900 ACTTCTTCCTTTTTCCTCCTTCTG 58.619 41.667 0.00 0.00 0.00 3.02
171 214 5.654901 ACTTCTTCCTTTTTCCTCCTTCT 57.345 39.130 0.00 0.00 0.00 2.85
172 215 6.999272 ACTTACTTCTTCCTTTTTCCTCCTTC 59.001 38.462 0.00 0.00 0.00 3.46
173 216 6.773200 CACTTACTTCTTCCTTTTTCCTCCTT 59.227 38.462 0.00 0.00 0.00 3.36
175 218 6.296803 TCACTTACTTCTTCCTTTTTCCTCC 58.703 40.000 0.00 0.00 0.00 4.30
179 222 7.803279 TCCTTCACTTACTTCTTCCTTTTTC 57.197 36.000 0.00 0.00 0.00 2.29
180 223 8.589701 TTTCCTTCACTTACTTCTTCCTTTTT 57.410 30.769 0.00 0.00 0.00 1.94
184 227 6.502074 ACTTTCCTTCACTTACTTCTTCCT 57.498 37.500 0.00 0.00 0.00 3.36
185 228 7.443477 ACTACTTTCCTTCACTTACTTCTTCC 58.557 38.462 0.00 0.00 0.00 3.46
187 230 9.930693 CATACTACTTTCCTTCACTTACTTCTT 57.069 33.333 0.00 0.00 0.00 2.52
189 232 9.575783 CTCATACTACTTTCCTTCACTTACTTC 57.424 37.037 0.00 0.00 0.00 3.01
192 235 6.757478 GCCTCATACTACTTTCCTTCACTTAC 59.243 42.308 0.00 0.00 0.00 2.34
193 236 6.668283 AGCCTCATACTACTTTCCTTCACTTA 59.332 38.462 0.00 0.00 0.00 2.24
194 237 5.485708 AGCCTCATACTACTTTCCTTCACTT 59.514 40.000 0.00 0.00 0.00 3.16
195 238 5.026790 AGCCTCATACTACTTTCCTTCACT 58.973 41.667 0.00 0.00 0.00 3.41
197 240 5.023452 TCAGCCTCATACTACTTTCCTTCA 58.977 41.667 0.00 0.00 0.00 3.02
198 241 5.599999 TCAGCCTCATACTACTTTCCTTC 57.400 43.478 0.00 0.00 0.00 3.46
199 242 5.426833 ACATCAGCCTCATACTACTTTCCTT 59.573 40.000 0.00 0.00 0.00 3.36
202 245 5.907207 TCACATCAGCCTCATACTACTTTC 58.093 41.667 0.00 0.00 0.00 2.62
321 365 0.511221 CAGAGGTAAAACCGTGCACG 59.489 55.000 31.77 31.77 44.90 5.34
323 367 2.624169 GCAGAGGTAAAACCGTGCA 58.376 52.632 16.85 0.00 46.18 4.57
326 370 2.034179 GCTTTTGCAGAGGTAAAACCGT 59.966 45.455 1.94 0.00 44.20 4.83
346 390 0.321671 TTGTGTGAGGCAGAGTAGGC 59.678 55.000 0.00 0.00 0.00 3.93
365 409 4.948004 GCAGGTTTAATTAAGCAGGTAGGT 59.052 41.667 13.23 0.00 36.70 3.08
371 415 3.427503 CGGTGGCAGGTTTAATTAAGCAG 60.428 47.826 13.23 6.83 36.70 4.24
380 424 3.272581 GTTATTAGCGGTGGCAGGTTTA 58.727 45.455 0.00 0.00 43.41 2.01
441 485 1.437573 CTCTTATCTGGCGCGTCCA 59.562 57.895 18.85 18.85 44.18 4.02
615 667 4.725556 TGCTTGAACGTGTAAATGTCTC 57.274 40.909 0.00 0.00 0.00 3.36
912 1715 9.806203 CGATATATATATAGAGAGACGTAGGGG 57.194 40.741 5.19 0.00 0.00 4.79
927 1730 7.891183 GGATGTGGAGGGAGACGATATATATAT 59.109 40.741 4.86 4.86 0.00 0.86
1569 2532 9.797732 TCCATACAGGATTATATTCCAGGATTA 57.202 33.333 14.57 0.00 43.07 1.75
1570 2533 8.700145 TCCATACAGGATTATATTCCAGGATT 57.300 34.615 14.57 0.00 43.07 3.01
1628 2852 0.318614 GTCCCAAATTGTGTGCCGTG 60.319 55.000 0.00 0.00 0.00 4.94
1676 2907 1.335810 ACATTGATGCACGATGGATGC 59.664 47.619 16.18 0.00 42.88 3.91
1786 3017 8.482429 GCAACAATAATATAATCTTGCACTTGC 58.518 33.333 0.00 0.00 42.50 4.01
1836 3067 4.790051 TACGTGTGGGCGTATTCG 57.210 55.556 0.00 0.00 45.06 3.34
1927 3158 0.847670 TTGTGACGTTTCGCTGTACG 59.152 50.000 0.00 0.00 45.62 3.67
2072 3313 2.124983 CTGCCTGACCGGACATGG 60.125 66.667 9.46 13.02 33.16 3.66
2080 3321 2.433318 GACGCTGACTGCCTGACC 60.433 66.667 0.00 0.00 38.78 4.02
2172 3417 0.320050 GCATCTTTCCCCCGCAAAAA 59.680 50.000 0.00 0.00 0.00 1.94
2173 3418 0.829602 TGCATCTTTCCCCCGCAAAA 60.830 50.000 0.00 0.00 0.00 2.44
2174 3419 1.228706 TGCATCTTTCCCCCGCAAA 60.229 52.632 0.00 0.00 0.00 3.68
2175 3420 1.678635 CTGCATCTTTCCCCCGCAA 60.679 57.895 0.00 0.00 31.10 4.85
2176 3421 2.045045 CTGCATCTTTCCCCCGCA 60.045 61.111 0.00 0.00 0.00 5.69
2177 3422 2.115291 GTCTGCATCTTTCCCCCGC 61.115 63.158 0.00 0.00 0.00 6.13
2178 3423 0.035056 AAGTCTGCATCTTTCCCCCG 60.035 55.000 0.00 0.00 0.00 5.73
2179 3424 1.756430 GAAGTCTGCATCTTTCCCCC 58.244 55.000 5.90 0.00 0.00 5.40
2180 3425 1.373570 CGAAGTCTGCATCTTTCCCC 58.626 55.000 5.90 0.00 0.00 4.81
2181 3426 1.066143 TCCGAAGTCTGCATCTTTCCC 60.066 52.381 5.90 0.00 0.00 3.97
2182 3427 2.386661 TCCGAAGTCTGCATCTTTCC 57.613 50.000 5.90 0.00 0.00 3.13
2183 3428 4.749245 TTTTCCGAAGTCTGCATCTTTC 57.251 40.909 5.90 1.15 0.00 2.62
2184 3429 5.464168 CAATTTTCCGAAGTCTGCATCTTT 58.536 37.500 5.90 0.00 0.00 2.52
2185 3430 4.082571 CCAATTTTCCGAAGTCTGCATCTT 60.083 41.667 4.33 4.33 0.00 2.40
2186 3431 3.441572 CCAATTTTCCGAAGTCTGCATCT 59.558 43.478 0.00 0.00 0.00 2.90
2187 3432 3.762779 CCAATTTTCCGAAGTCTGCATC 58.237 45.455 0.00 0.00 0.00 3.91
2188 3433 2.094545 GCCAATTTTCCGAAGTCTGCAT 60.095 45.455 0.00 0.00 0.00 3.96
2189 3434 1.269448 GCCAATTTTCCGAAGTCTGCA 59.731 47.619 0.00 0.00 0.00 4.41
2190 3435 1.402852 GGCCAATTTTCCGAAGTCTGC 60.403 52.381 0.00 0.00 0.00 4.26
2191 3436 1.885887 TGGCCAATTTTCCGAAGTCTG 59.114 47.619 0.61 0.00 0.00 3.51
2192 3437 1.886542 GTGGCCAATTTTCCGAAGTCT 59.113 47.619 7.24 0.00 0.00 3.24
2193 3438 1.401018 CGTGGCCAATTTTCCGAAGTC 60.401 52.381 7.24 0.00 0.00 3.01
2194 3439 0.596082 CGTGGCCAATTTTCCGAAGT 59.404 50.000 7.24 0.00 0.00 3.01
2195 3440 0.878416 TCGTGGCCAATTTTCCGAAG 59.122 50.000 7.24 0.00 0.00 3.79
2196 3441 1.201181 CATCGTGGCCAATTTTCCGAA 59.799 47.619 16.54 2.64 0.00 4.30
2197 3442 0.808125 CATCGTGGCCAATTTTCCGA 59.192 50.000 7.24 12.34 0.00 4.55
2198 3443 0.808125 TCATCGTGGCCAATTTTCCG 59.192 50.000 7.24 5.79 0.00 4.30
2211 3456 7.755822 GGATTATCGTAAGCTTAGAATCATCGT 59.244 37.037 20.76 9.61 37.18 3.73
2212 3457 7.971168 AGGATTATCGTAAGCTTAGAATCATCG 59.029 37.037 20.76 14.28 37.18 3.84
2257 3502 6.813152 GGTAACATTTGGTTGGAAATCATGAG 59.187 38.462 0.09 0.00 36.42 2.90
2401 3646 9.246670 ACCTTGATGTTTGATGAATAGATTGAA 57.753 29.630 0.00 0.00 0.00 2.69
2402 3647 8.812513 ACCTTGATGTTTGATGAATAGATTGA 57.187 30.769 0.00 0.00 0.00 2.57
2404 3649 9.911788 ACTACCTTGATGTTTGATGAATAGATT 57.088 29.630 0.00 0.00 0.00 2.40
2406 3651 9.817809 GTACTACCTTGATGTTTGATGAATAGA 57.182 33.333 0.00 0.00 0.00 1.98
2407 3652 9.599866 TGTACTACCTTGATGTTTGATGAATAG 57.400 33.333 0.00 0.00 0.00 1.73
2408 3653 9.952030 TTGTACTACCTTGATGTTTGATGAATA 57.048 29.630 0.00 0.00 0.00 1.75
2409 3654 8.862325 TTGTACTACCTTGATGTTTGATGAAT 57.138 30.769 0.00 0.00 0.00 2.57
2410 3655 8.684386 TTTGTACTACCTTGATGTTTGATGAA 57.316 30.769 0.00 0.00 0.00 2.57
2411 3656 8.684386 TTTTGTACTACCTTGATGTTTGATGA 57.316 30.769 0.00 0.00 0.00 2.92
2412 3657 9.180678 GTTTTTGTACTACCTTGATGTTTGATG 57.819 33.333 0.00 0.00 0.00 3.07
2413 3658 8.908903 TGTTTTTGTACTACCTTGATGTTTGAT 58.091 29.630 0.00 0.00 0.00 2.57
2414 3659 8.282455 TGTTTTTGTACTACCTTGATGTTTGA 57.718 30.769 0.00 0.00 0.00 2.69
2416 3661 8.908903 TGATGTTTTTGTACTACCTTGATGTTT 58.091 29.630 0.00 0.00 0.00 2.83
2417 3662 8.458573 TGATGTTTTTGTACTACCTTGATGTT 57.541 30.769 0.00 0.00 0.00 2.71
2418 3663 7.936847 TCTGATGTTTTTGTACTACCTTGATGT 59.063 33.333 0.00 0.00 0.00 3.06
2419 3664 8.322906 TCTGATGTTTTTGTACTACCTTGATG 57.677 34.615 0.00 0.00 0.00 3.07
2420 3665 8.918202 TTCTGATGTTTTTGTACTACCTTGAT 57.082 30.769 0.00 0.00 0.00 2.57
2421 3666 8.617809 GTTTCTGATGTTTTTGTACTACCTTGA 58.382 33.333 0.00 0.00 0.00 3.02
2423 3668 8.514330 TGTTTCTGATGTTTTTGTACTACCTT 57.486 30.769 0.00 0.00 0.00 3.50
2424 3669 8.403236 GTTGTTTCTGATGTTTTTGTACTACCT 58.597 33.333 0.00 0.00 0.00 3.08
2425 3670 8.185505 TGTTGTTTCTGATGTTTTTGTACTACC 58.814 33.333 0.00 0.00 0.00 3.18
2426 3671 9.562583 TTGTTGTTTCTGATGTTTTTGTACTAC 57.437 29.630 0.00 0.00 0.00 2.73
2428 3673 9.482627 TTTTGTTGTTTCTGATGTTTTTGTACT 57.517 25.926 0.00 0.00 0.00 2.73
2437 3682 9.260002 GGATGTAATTTTTGTTGTTTCTGATGT 57.740 29.630 0.00 0.00 0.00 3.06
2438 3683 9.258826 TGGATGTAATTTTTGTTGTTTCTGATG 57.741 29.630 0.00 0.00 0.00 3.07
2440 3685 9.258826 CATGGATGTAATTTTTGTTGTTTCTGA 57.741 29.630 0.00 0.00 0.00 3.27
2441 3686 9.044150 ACATGGATGTAATTTTTGTTGTTTCTG 57.956 29.630 0.00 0.00 39.68 3.02
2445 3690 9.995003 ACATACATGGATGTAATTTTTGTTGTT 57.005 25.926 22.45 0.00 45.40 2.83
2450 3695 7.867403 GGCCTACATACATGGATGTAATTTTTG 59.133 37.037 27.00 16.14 45.40 2.44
2451 3696 7.563188 TGGCCTACATACATGGATGTAATTTTT 59.437 33.333 27.00 6.24 45.40 1.94
2452 3697 7.014230 GTGGCCTACATACATGGATGTAATTTT 59.986 37.037 27.00 6.92 45.40 1.82
2453 3698 6.490040 GTGGCCTACATACATGGATGTAATTT 59.510 38.462 27.00 7.61 45.40 1.82
2455 3700 5.514834 GGTGGCCTACATACATGGATGTAAT 60.515 44.000 27.00 8.31 45.40 1.89
2458 3703 2.106511 GGTGGCCTACATACATGGATGT 59.893 50.000 26.41 26.41 42.68 3.06
2459 3704 2.373169 AGGTGGCCTACATACATGGATG 59.627 50.000 16.79 16.79 28.47 3.51
2460 3705 2.706350 AGGTGGCCTACATACATGGAT 58.294 47.619 3.32 0.00 28.47 3.41
2461 3706 2.190398 AGGTGGCCTACATACATGGA 57.810 50.000 3.32 0.00 28.47 3.41
2463 3708 2.368548 TGCTAGGTGGCCTACATACATG 59.631 50.000 3.32 0.00 34.61 3.21
2464 3709 2.689658 TGCTAGGTGGCCTACATACAT 58.310 47.619 3.32 0.00 34.61 2.29
2465 3710 2.168458 TGCTAGGTGGCCTACATACA 57.832 50.000 3.32 2.02 34.61 2.29
2467 3712 2.473070 TGTTGCTAGGTGGCCTACATA 58.527 47.619 3.32 1.78 34.61 2.29
2468 3713 1.285280 TGTTGCTAGGTGGCCTACAT 58.715 50.000 3.32 0.45 34.61 2.29
2470 3715 2.420058 ATTGTTGCTAGGTGGCCTAC 57.580 50.000 3.32 0.00 34.61 3.18
2471 3716 3.264706 TGTAATTGTTGCTAGGTGGCCTA 59.735 43.478 3.32 0.00 34.61 3.93
2472 3717 2.041081 TGTAATTGTTGCTAGGTGGCCT 59.959 45.455 3.32 0.00 37.71 5.19
2473 3718 2.442413 TGTAATTGTTGCTAGGTGGCC 58.558 47.619 0.00 0.00 0.00 5.36
2474 3719 3.673323 GCTTGTAATTGTTGCTAGGTGGC 60.673 47.826 0.00 0.00 0.00 5.01
2478 3723 5.104374 CCAATGCTTGTAATTGTTGCTAGG 58.896 41.667 0.00 0.00 33.93 3.02
2479 3724 5.953183 TCCAATGCTTGTAATTGTTGCTAG 58.047 37.500 0.00 0.00 33.93 3.42
2480 3725 5.622007 GCTCCAATGCTTGTAATTGTTGCTA 60.622 40.000 0.00 0.00 33.93 3.49
2481 3726 4.813027 CTCCAATGCTTGTAATTGTTGCT 58.187 39.130 0.00 0.00 33.93 3.91
2484 3729 3.505680 TCGCTCCAATGCTTGTAATTGTT 59.494 39.130 0.00 0.00 33.93 2.83
2485 3730 3.081061 TCGCTCCAATGCTTGTAATTGT 58.919 40.909 0.00 0.00 33.93 2.71
2486 3731 3.688272 CTCGCTCCAATGCTTGTAATTG 58.312 45.455 0.00 0.00 35.26 2.32
2487 3732 2.098117 GCTCGCTCCAATGCTTGTAATT 59.902 45.455 0.00 0.00 0.00 1.40
2488 3733 1.672881 GCTCGCTCCAATGCTTGTAAT 59.327 47.619 0.00 0.00 0.00 1.89
2490 3735 0.250234 AGCTCGCTCCAATGCTTGTA 59.750 50.000 0.00 0.00 30.96 2.41
2492 3737 1.022982 TCAGCTCGCTCCAATGCTTG 61.023 55.000 0.00 0.00 33.03 4.01
2493 3738 0.321919 TTCAGCTCGCTCCAATGCTT 60.322 50.000 0.00 0.00 33.03 3.91
2494 3739 0.743701 CTTCAGCTCGCTCCAATGCT 60.744 55.000 0.00 0.00 36.04 3.79
2495 3740 1.720301 CTTCAGCTCGCTCCAATGC 59.280 57.895 0.00 0.00 0.00 3.56
2497 3742 1.451028 GGCTTCAGCTCGCTCCAAT 60.451 57.895 0.00 0.00 41.70 3.16
2498 3743 2.046892 GGCTTCAGCTCGCTCCAA 60.047 61.111 0.00 0.00 41.70 3.53
2499 3744 4.441695 CGGCTTCAGCTCGCTCCA 62.442 66.667 0.00 0.00 41.70 3.86
2507 3752 3.885521 GATGGCAGCGGCTTCAGC 61.886 66.667 9.17 0.01 40.87 4.26
2509 3754 0.533531 CTATGATGGCAGCGGCTTCA 60.534 55.000 9.17 14.47 43.74 3.02
2510 3755 1.849976 GCTATGATGGCAGCGGCTTC 61.850 60.000 9.17 9.49 40.87 3.86
2511 3756 1.895707 GCTATGATGGCAGCGGCTT 60.896 57.895 9.17 0.00 40.87 4.35
2512 3757 2.281345 GCTATGATGGCAGCGGCT 60.281 61.111 9.17 0.00 40.87 5.52
2514 3759 2.670934 GGGCTATGATGGCAGCGG 60.671 66.667 2.55 0.00 38.73 5.52
2515 3760 2.670934 GGGGCTATGATGGCAGCG 60.671 66.667 2.55 0.00 38.73 5.18
2517 3762 1.377994 GGAGGGGCTATGATGGCAG 59.622 63.158 2.55 0.00 0.00 4.85
2518 3763 2.156098 GGGAGGGGCTATGATGGCA 61.156 63.158 2.55 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.