Multiple sequence alignment - TraesCS5B01G542300

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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 TraesCS5B01G542300 chr5B 100.000 4108 0 0 1 4108 696179399 696175292 0.000000e+00 7587.0
1 TraesCS5B01G542300 chr5B 79.139 604 63 28 1844 2421 690650186 690649620 3.900000e-95 359.0
2 TraesCS5B01G542300 chr5D 91.558 2464 145 28 1695 4108 554505503 554507953 0.000000e+00 3339.0
3 TraesCS5B01G542300 chr5D 87.930 1135 49 30 591 1687 554504353 554505437 0.000000e+00 1256.0
4 TraesCS5B01G542300 chr5D 78.808 604 76 23 1844 2421 6111498 6110921 3.900000e-95 359.0
5 TraesCS5B01G542300 chr5D 85.714 357 21 13 1 347 554503702 554504038 2.350000e-92 350.0
6 TraesCS5B01G542300 chr5D 88.793 116 12 1 476 591 554504071 554504185 1.540000e-29 141.0
7 TraesCS5B01G542300 chr4A 92.223 2096 103 18 2037 4108 614028558 614026499 0.000000e+00 2913.0
8 TraesCS5B01G542300 chr4A 92.439 820 33 14 777 1578 614029978 614029170 0.000000e+00 1144.0
9 TraesCS5B01G542300 chr4A 85.122 410 23 21 1 388 614030828 614030435 6.440000e-103 385.0
10 TraesCS5B01G542300 chr4A 90.612 245 12 6 1796 2037 614028980 614028744 8.570000e-82 315.0
11 TraesCS5B01G542300 chr4A 92.727 110 8 0 488 597 614030421 614030312 4.250000e-35 159.0
12 TraesCS5B01G542300 chr4A 95.238 42 1 1 2439 2479 719098249 719098208 9.530000e-07 65.8
13 TraesCS5B01G542300 chr1A 79.667 600 61 26 1848 2421 590841639 590841075 3.880000e-100 375.0
14 TraesCS5B01G542300 chr1A 97.917 96 2 0 383 478 577481115 577481210 2.540000e-37 167.0
15 TraesCS5B01G542300 chr1A 96.739 92 3 0 383 474 409786914 409787005 1.980000e-33 154.0
16 TraesCS5B01G542300 chr1A 85.897 78 9 2 2496 2573 590841052 590840977 9.460000e-12 82.4
17 TraesCS5B01G542300 chr2B 88.889 171 17 2 1407 1577 674066724 674066556 4.160000e-50 209.0
18 TraesCS5B01G542300 chr2B 92.157 51 3 1 2430 2479 458853936 458853986 2.050000e-08 71.3
19 TraesCS5B01G542300 chr2B 95.455 44 1 1 2443 2485 265428469 265428426 7.370000e-08 69.4
20 TraesCS5B01G542300 chr4B 87.719 171 19 2 1407 1577 563997714 563997546 9.010000e-47 198.0
21 TraesCS5B01G542300 chr3B 86.096 187 22 4 1392 1578 543184176 543184358 9.010000e-47 198.0
22 TraesCS5B01G542300 chr7A 96.809 94 3 0 384 477 138960830 138960737 1.530000e-34 158.0
23 TraesCS5B01G542300 chr7A 96.809 94 1 2 387 480 471816184 471816093 5.500000e-34 156.0
24 TraesCS5B01G542300 chr3D 98.851 87 1 0 387 473 497727997 497727911 5.500000e-34 156.0
25 TraesCS5B01G542300 chr3D 97.753 89 2 0 386 474 129678090 129678002 1.980000e-33 154.0
26 TraesCS5B01G542300 chr3D 90.385 52 3 2 2442 2491 486153959 486154010 2.650000e-07 67.6
27 TraesCS5B01G542300 chr6A 97.753 89 2 0 387 475 158080479 158080391 1.980000e-33 154.0
28 TraesCS5B01G542300 chrUn 95.699 93 4 0 384 476 22143156 22143248 2.560000e-32 150.0
29 TraesCS5B01G542300 chr1B 93.000 100 5 2 375 474 490725748 490725845 1.190000e-30 145.0
30 TraesCS5B01G542300 chr1B 97.619 42 0 1 2440 2480 338014806 338014765 2.050000e-08 71.3
31 TraesCS5B01G542300 chr5A 95.652 46 1 1 2436 2480 76958145 76958190 5.700000e-09 73.1
32 TraesCS5B01G542300 chr4D 97.500 40 1 0 2440 2479 360939795 360939834 7.370000e-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 TraesCS5B01G542300 chr5B 696175292 696179399 4107 True 7587.0 7587 100.00000 1 4108 1 chr5B.!!$R2 4107
1 TraesCS5B01G542300 chr5B 690649620 690650186 566 True 359.0 359 79.13900 1844 2421 1 chr5B.!!$R1 577
2 TraesCS5B01G542300 chr5D 554503702 554507953 4251 False 1271.5 3339 88.49875 1 4108 4 chr5D.!!$F1 4107
3 TraesCS5B01G542300 chr5D 6110921 6111498 577 True 359.0 359 78.80800 1844 2421 1 chr5D.!!$R1 577
4 TraesCS5B01G542300 chr4A 614026499 614030828 4329 True 983.2 2913 90.62460 1 4108 5 chr4A.!!$R2 4107
5 TraesCS5B01G542300 chr1A 590840977 590841639 662 True 228.7 375 82.78200 1848 2573 2 chr1A.!!$R1 725

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 1071 0.099082 GTGACGGTTCGCCAAAACAA 59.901 50.000 0.0 0.0 37.0 2.83 F
831 1082 1.298788 CAAAACAACACCCGTCGCC 60.299 57.895 0.0 0.0 0.0 5.54 F
1002 1260 1.370437 CTCTGCTCCCGATCCCATG 59.630 63.158 0.0 0.0 0.0 3.66 F
1891 2239 0.729140 GCGACCTTGATTTTGCCGTG 60.729 55.000 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1664 1940 0.972883 GGGCCAAAAACTATGTGCCA 59.027 50.000 4.39 0.0 36.46 4.92 R
1665 1941 0.972883 TGGGCCAAAAACTATGTGCC 59.027 50.000 2.13 0.0 35.00 5.01 R
2986 3530 1.610522 CCAAACTTTCCTGCTCCACAG 59.389 52.381 0.00 0.0 46.77 3.66 R
3829 4392 0.255890 TGTAGGAAGAGCCATTGCCC 59.744 55.000 0.00 0.0 40.02 5.36 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
23 24 0.107456 AGCACAGAACCAGGTGAGTG 59.893 55.000 12.74 12.74 37.18 3.51
45 47 7.948357 AGTGTTTATGTAACTAGTCACTCACA 58.052 34.615 0.00 0.00 37.64 3.58
77 79 5.841957 AGTTAAATGTGGATCTGGATTGC 57.158 39.130 0.00 0.00 0.00 3.56
116 118 3.624326 TTATGTGCTGTTTGCTGTCAC 57.376 42.857 0.00 0.00 43.37 3.67
120 122 1.003116 GTGCTGTTTGCTGTCACAGAG 60.003 52.381 9.70 0.00 42.74 3.35
124 126 2.288666 TGTTTGCTGTCACAGAGAACC 58.711 47.619 9.70 0.00 32.44 3.62
144 151 4.318332 ACCAGTAGTCATCATGTGTGTTG 58.682 43.478 0.00 0.00 0.00 3.33
148 155 5.062683 CAGTAGTCATCATGTGTGTTGTAGC 59.937 44.000 0.00 0.00 0.00 3.58
176 183 1.603456 TGCTGCAATTTCCTGTCGAA 58.397 45.000 0.00 0.00 0.00 3.71
178 185 2.162208 TGCTGCAATTTCCTGTCGAATC 59.838 45.455 0.00 0.00 0.00 2.52
184 191 0.672401 TTTCCTGTCGAATCCGTGCC 60.672 55.000 0.00 0.00 37.05 5.01
185 192 2.829043 TTCCTGTCGAATCCGTGCCG 62.829 60.000 0.00 0.00 37.05 5.69
245 252 2.012937 TGCTGCCAAAATAGCATTGC 57.987 45.000 0.00 0.00 44.36 3.56
246 253 1.275573 TGCTGCCAAAATAGCATTGCA 59.724 42.857 11.91 0.00 44.36 4.08
247 254 2.093394 TGCTGCCAAAATAGCATTGCAT 60.093 40.909 11.91 0.00 44.36 3.96
248 255 2.940410 GCTGCCAAAATAGCATTGCATT 59.060 40.909 11.91 6.02 40.04 3.56
249 256 3.242608 GCTGCCAAAATAGCATTGCATTG 60.243 43.478 11.91 9.84 40.04 2.82
250 257 2.678836 TGCCAAAATAGCATTGCATTGC 59.321 40.909 22.79 22.79 43.09 3.56
303 322 7.558444 GGTGATAATAACATCAGGGTGGTAAAA 59.442 37.037 0.00 0.00 35.63 1.52
349 375 0.302890 CGAGCCGATGAACATCTTGC 59.697 55.000 12.05 13.15 35.72 4.01
351 377 1.739466 GAGCCGATGAACATCTTGCAA 59.261 47.619 19.86 0.00 36.40 4.08
352 378 2.161855 AGCCGATGAACATCTTGCAAA 58.838 42.857 19.86 0.00 36.40 3.68
353 379 2.756760 AGCCGATGAACATCTTGCAAAT 59.243 40.909 19.86 0.00 36.40 2.32
354 380 3.194116 AGCCGATGAACATCTTGCAAATT 59.806 39.130 19.86 0.00 36.40 1.82
355 381 4.398988 AGCCGATGAACATCTTGCAAATTA 59.601 37.500 19.86 0.00 36.40 1.40
356 382 5.068198 AGCCGATGAACATCTTGCAAATTAT 59.932 36.000 19.86 0.00 36.40 1.28
381 412 2.732016 CTTTGCTTGCTGCTGCCA 59.268 55.556 13.47 0.57 43.37 4.92
383 414 0.528924 CTTTGCTTGCTGCTGCCATA 59.471 50.000 13.47 0.00 43.37 2.74
395 426 2.008242 CTGCCATAGCTACTCCCTCT 57.992 55.000 0.00 0.00 40.80 3.69
396 427 1.617850 CTGCCATAGCTACTCCCTCTG 59.382 57.143 0.00 0.00 40.80 3.35
397 428 1.062886 TGCCATAGCTACTCCCTCTGT 60.063 52.381 0.00 0.00 40.80 3.41
398 429 2.177016 TGCCATAGCTACTCCCTCTGTA 59.823 50.000 0.00 0.00 40.80 2.74
399 430 3.231818 GCCATAGCTACTCCCTCTGTAA 58.768 50.000 0.00 0.00 35.50 2.41
400 431 3.641906 GCCATAGCTACTCCCTCTGTAAA 59.358 47.826 0.00 0.00 35.50 2.01
401 432 4.501743 GCCATAGCTACTCCCTCTGTAAAC 60.502 50.000 0.00 0.00 35.50 2.01
402 433 4.896482 CCATAGCTACTCCCTCTGTAAACT 59.104 45.833 0.00 0.00 0.00 2.66
403 434 6.069331 CCATAGCTACTCCCTCTGTAAACTA 58.931 44.000 0.00 0.00 0.00 2.24
404 435 6.550108 CCATAGCTACTCCCTCTGTAAACTAA 59.450 42.308 0.00 0.00 0.00 2.24
405 436 7.233757 CCATAGCTACTCCCTCTGTAAACTAAT 59.766 40.741 0.00 0.00 0.00 1.73
406 437 9.298250 CATAGCTACTCCCTCTGTAAACTAATA 57.702 37.037 0.00 0.00 0.00 0.98
409 440 9.878737 AGCTACTCCCTCTGTAAACTAATATAA 57.121 33.333 0.00 0.00 0.00 0.98
413 444 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
414 445 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
415 446 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
465 496 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
466 497 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
467 498 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
468 499 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
469 500 8.003629 ACTCTTATATTAGTTTACGGAGGGAGT 58.996 37.037 0.00 0.00 0.00 3.85
470 501 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
471 502 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
472 503 9.294614 CTTATATTAGTTTACGGAGGGAGTACT 57.705 37.037 0.00 0.00 0.00 2.73
473 504 9.646522 TTATATTAGTTTACGGAGGGAGTACTT 57.353 33.333 0.00 0.00 0.00 2.24
474 505 5.904362 TTAGTTTACGGAGGGAGTACTTC 57.096 43.478 0.00 0.00 0.00 3.01
475 506 4.044946 AGTTTACGGAGGGAGTACTTCT 57.955 45.455 0.01 0.06 0.00 2.85
476 507 4.414677 AGTTTACGGAGGGAGTACTTCTT 58.585 43.478 0.01 0.00 0.00 2.52
477 508 5.574188 AGTTTACGGAGGGAGTACTTCTTA 58.426 41.667 0.01 0.00 0.00 2.10
484 515 4.140876 GGAGGGAGTACTTCTTATCCTCCT 60.141 50.000 23.26 9.79 44.78 3.69
485 516 5.069518 AGGGAGTACTTCTTATCCTCCTC 57.930 47.826 0.01 0.00 41.20 3.71
486 517 4.482772 AGGGAGTACTTCTTATCCTCCTCA 59.517 45.833 0.01 0.00 41.20 3.86
545 576 2.890371 GGCCACGTACTGGTCGAT 59.110 61.111 0.00 0.00 42.99 3.59
549 580 0.525668 CCACGTACTGGTCGATGAGC 60.526 60.000 0.00 0.00 34.90 4.26
756 1007 4.821589 GGAGGCGAGCAAGACCCG 62.822 72.222 0.00 0.00 0.00 5.28
789 1040 3.943479 TTTGGCATCGACCGACGGG 62.943 63.158 20.00 0.62 42.82 5.28
820 1071 0.099082 GTGACGGTTCGCCAAAACAA 59.901 50.000 0.00 0.00 37.00 2.83
821 1072 0.099082 TGACGGTTCGCCAAAACAAC 59.901 50.000 0.00 0.00 37.00 3.32
831 1082 1.298788 CAAAACAACACCCGTCGCC 60.299 57.895 0.00 0.00 0.00 5.54
913 1164 1.891060 GAGCCGCCGCAATCTTATCG 61.891 60.000 0.00 0.00 37.52 2.92
938 1189 2.125512 CGTCGCCTCCCTCCAAAG 60.126 66.667 0.00 0.00 0.00 2.77
1002 1260 1.370437 CTCTGCTCCCGATCCCATG 59.630 63.158 0.00 0.00 0.00 3.66
1003 1261 2.109517 CTCTGCTCCCGATCCCATGG 62.110 65.000 4.14 4.14 0.00 3.66
1004 1262 3.839353 CTGCTCCCGATCCCATGGC 62.839 68.421 6.09 0.00 0.00 4.40
1005 1263 4.996434 GCTCCCGATCCCATGGCG 62.996 72.222 6.09 4.56 0.00 5.69
1006 1264 4.320456 CTCCCGATCCCATGGCGG 62.320 72.222 19.20 19.20 44.42 6.13
1383 1659 3.791586 GCTCCCTCCTGCCTGGAC 61.792 72.222 0.00 0.00 40.56 4.02
1470 1746 2.815647 CGGCCAGTCTTCTTCCGC 60.816 66.667 2.24 0.00 33.07 5.54
1578 1854 1.869767 CTCATCTGCCGAATGGTAAGC 59.130 52.381 0.00 0.00 37.67 3.09
1582 1858 1.718757 CTGCCGAATGGTAAGCAGCC 61.719 60.000 0.00 0.00 45.44 4.85
1600 1876 2.629137 AGCCACAGATGTGCAAAATGAA 59.371 40.909 7.46 0.00 44.34 2.57
1637 1913 5.296283 GTCTGAATATGCTTCTTCAGTGCAT 59.704 40.000 20.26 12.22 45.49 3.96
1640 1916 6.585416 TGAATATGCTTCTTCAGTGCATCTA 58.415 36.000 11.34 0.46 44.91 1.98
1643 1919 4.750021 TGCTTCTTCAGTGCATCTATCT 57.250 40.909 0.00 0.00 0.00 1.98
1659 1935 9.159364 TGCATCTATCTGCTTGATTTACATATC 57.841 33.333 0.00 0.00 42.75 1.63
1687 1963 3.261580 GCACATAGTTTTTGGCCCATTC 58.738 45.455 0.00 0.00 0.00 2.67
1688 1964 3.055891 GCACATAGTTTTTGGCCCATTCT 60.056 43.478 0.00 0.00 0.00 2.40
1689 1965 4.563374 GCACATAGTTTTTGGCCCATTCTT 60.563 41.667 0.00 0.00 0.00 2.52
1692 1968 2.849942 AGTTTTTGGCCCATTCTTTGC 58.150 42.857 0.00 0.00 0.00 3.68
1693 1969 2.439135 AGTTTTTGGCCCATTCTTTGCT 59.561 40.909 0.00 0.00 0.00 3.91
1695 1971 1.714541 TTTGGCCCATTCTTTGCTCA 58.285 45.000 0.00 0.00 0.00 4.26
1696 1972 0.968405 TTGGCCCATTCTTTGCTCAC 59.032 50.000 0.00 0.00 0.00 3.51
1716 2054 2.026641 CGATGTTGAATTGGGGAGCAT 58.973 47.619 0.00 0.00 0.00 3.79
1775 2121 2.095110 TGTTTCGATGCTTCATGCCTTG 60.095 45.455 0.08 0.00 42.00 3.61
1787 2133 5.508200 TTCATGCCTTGAGTTACGTTTTT 57.492 34.783 0.00 0.00 35.27 1.94
1790 2136 4.545823 TGCCTTGAGTTACGTTTTTCAG 57.454 40.909 0.00 0.00 0.00 3.02
1841 2188 8.846943 TTTCAATTGCTTCAGTTACTGAGATA 57.153 30.769 14.99 0.14 41.75 1.98
1846 2193 5.955488 TGCTTCAGTTACTGAGATAGTGAC 58.045 41.667 14.99 0.00 44.02 3.67
1891 2239 0.729140 GCGACCTTGATTTTGCCGTG 60.729 55.000 0.00 0.00 0.00 4.94
1897 2245 2.493278 CCTTGATTTTGCCGTGGAGATT 59.507 45.455 0.00 0.00 0.00 2.40
1969 2317 2.812499 GTCCGCCTATCGCCTGAA 59.188 61.111 0.00 0.00 36.73 3.02
2018 2370 0.810031 ACTGACACTGTTCGCACACC 60.810 55.000 0.00 0.00 0.00 4.16
2032 2384 2.668457 CGCACACCTGTATTCTGACTTC 59.332 50.000 0.00 0.00 0.00 3.01
2332 2874 3.575351 GACTGAAGCTGGCGGTCGT 62.575 63.158 11.67 0.00 32.56 4.34
2422 2965 8.443953 AGCAATTTATCTAGTGATTGAGTTCC 57.556 34.615 11.48 0.00 34.32 3.62
2434 2977 5.123979 GTGATTGAGTTCCCAAATAGACACC 59.876 44.000 0.00 0.00 0.00 4.16
2438 2981 3.871594 GAGTTCCCAAATAGACACCATCG 59.128 47.826 0.00 0.00 0.00 3.84
2479 3023 7.542824 GTCTTACATTTTGAGACAGAGGAGTAC 59.457 40.741 0.00 0.00 39.59 2.73
2565 3109 8.772705 CCTTTGAAATCTCTATGATGTTAGCTC 58.227 37.037 0.00 0.00 35.21 4.09
3174 3718 8.918658 CACCAATCTGTATTTCTGTCAAAAATG 58.081 33.333 0.00 0.00 0.00 2.32
3194 3738 8.470040 AAAATGAGAATGATGTTGTACAATGC 57.530 30.769 12.26 5.08 0.00 3.56
3209 3753 5.820423 TGTACAATGCAAGTCTGTAACAACT 59.180 36.000 0.00 0.00 0.00 3.16
3316 3860 1.251251 ATGTTTGGACCAGCAGAAGC 58.749 50.000 0.00 0.00 42.56 3.86
3418 3963 3.192844 CAGTGATACTCAAGTGTACCGGT 59.807 47.826 13.98 13.98 0.00 5.28
3504 4057 6.530019 AGAACTATTAAATGTTTGGGCCAG 57.470 37.500 6.23 0.00 0.00 4.85
3554 4112 3.197983 TGAACCCATTGGAAGGATACCT 58.802 45.455 3.62 0.00 32.01 3.08
3596 4159 3.015675 TGTCAATCAATGGCAGCCATA 57.984 42.857 27.91 13.61 44.40 2.74
3664 4227 8.757982 ATATCCATACAAGAACAAGAAGCATT 57.242 30.769 0.00 0.00 0.00 3.56
3665 4228 6.258230 TCCATACAAGAACAAGAAGCATTG 57.742 37.500 0.00 0.00 36.22 2.82
3725 4288 5.428253 TGTTCAAGTTACTTGCAGTTCTCT 58.572 37.500 19.24 0.00 40.84 3.10
3728 4291 2.678324 AGTTACTTGCAGTTCTCTCGC 58.322 47.619 0.00 0.00 0.00 5.03
3779 4342 1.176527 GCAGCCAGCCAATTTGACTA 58.823 50.000 0.00 0.00 37.23 2.59
3811 4374 1.080025 GCTTGTCGCCCTTAGTCGT 60.080 57.895 0.00 0.00 0.00 4.34
3829 4392 2.106332 GTACCTGATGGGGACGCG 59.894 66.667 3.53 3.53 39.45 6.01
3849 4412 1.340991 GGGCAATGGCTCTTCCTACAA 60.341 52.381 6.78 0.00 37.60 2.41
3901 4464 0.179111 CGTCCGACTATGTGCATGGT 60.179 55.000 0.77 0.77 35.10 3.55
3960 4524 2.049063 GTCCTTGCGCTCGACACT 60.049 61.111 9.73 0.00 0.00 3.55
3961 4525 2.049156 TCCTTGCGCTCGACACTG 60.049 61.111 9.73 0.00 0.00 3.66
4032 4596 3.845781 TCAAGTTGGCAGACTCTTCTT 57.154 42.857 2.34 0.00 0.00 2.52
4036 4600 0.250901 TTGGCAGACTCTTCTTGCCC 60.251 55.000 11.77 0.00 41.64 5.36
4098 4662 1.301874 TTTGCGTCCCACCTTACCG 60.302 57.895 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 118 5.107824 CACATGATGACTACTGGTTCTCTG 58.892 45.833 0.00 0.00 0.00 3.35
120 122 4.569943 ACACACATGATGACTACTGGTTC 58.430 43.478 0.00 0.00 0.00 3.62
124 126 5.062683 GCTACAACACACATGATGACTACTG 59.937 44.000 0.00 0.00 33.05 2.74
144 151 0.168788 TGCAGCAAAAGCATCGCTAC 59.831 50.000 0.00 0.00 38.25 3.58
148 155 2.093152 GGAAATTGCAGCAAAAGCATCG 59.907 45.455 12.97 0.00 42.33 3.84
242 249 3.129813 GGTGATTCTCATGAGCAATGCAA 59.870 43.478 18.36 6.30 36.11 4.08
245 252 3.945921 ACTGGTGATTCTCATGAGCAATG 59.054 43.478 18.36 8.59 37.66 2.82
246 253 4.232188 ACTGGTGATTCTCATGAGCAAT 57.768 40.909 18.36 16.79 0.00 3.56
247 254 3.708403 ACTGGTGATTCTCATGAGCAA 57.292 42.857 18.36 12.99 0.00 3.91
248 255 3.431346 GCTACTGGTGATTCTCATGAGCA 60.431 47.826 18.36 7.83 0.00 4.26
249 256 3.129871 GCTACTGGTGATTCTCATGAGC 58.870 50.000 18.36 4.87 0.00 4.26
250 257 3.133542 TGGCTACTGGTGATTCTCATGAG 59.866 47.826 17.07 17.07 0.00 2.90
251 258 3.106827 TGGCTACTGGTGATTCTCATGA 58.893 45.455 0.00 0.00 0.00 3.07
252 259 3.548745 TGGCTACTGGTGATTCTCATG 57.451 47.619 0.00 0.00 0.00 3.07
253 260 4.785346 AATGGCTACTGGTGATTCTCAT 57.215 40.909 0.00 0.00 0.00 2.90
254 261 5.396772 CCTTAATGGCTACTGGTGATTCTCA 60.397 44.000 0.00 0.00 0.00 3.27
255 262 5.059833 CCTTAATGGCTACTGGTGATTCTC 58.940 45.833 0.00 0.00 0.00 2.87
256 263 4.475016 ACCTTAATGGCTACTGGTGATTCT 59.525 41.667 0.00 0.00 40.22 2.40
264 271 8.902540 TGTTATTATCACCTTAATGGCTACTG 57.097 34.615 0.00 0.00 40.22 2.74
271 281 8.786898 CACCCTGATGTTATTATCACCTTAATG 58.213 37.037 0.00 0.00 33.71 1.90
303 322 9.758651 TGCTGAATATTCGTACTATACATGTTT 57.241 29.630 2.30 0.00 0.00 2.83
312 331 4.534168 GCTCGTGCTGAATATTCGTACTA 58.466 43.478 18.38 11.50 36.03 1.82
313 332 3.372954 GCTCGTGCTGAATATTCGTACT 58.627 45.455 18.38 0.00 36.03 2.73
349 375 4.824479 AGCAAAGGGGGTCAATAATTTG 57.176 40.909 0.00 0.00 0.00 2.32
351 377 3.055167 GCAAGCAAAGGGGGTCAATAATT 60.055 43.478 0.00 0.00 0.00 1.40
352 378 2.501316 GCAAGCAAAGGGGGTCAATAAT 59.499 45.455 0.00 0.00 0.00 1.28
353 379 1.899142 GCAAGCAAAGGGGGTCAATAA 59.101 47.619 0.00 0.00 0.00 1.40
354 380 1.077005 AGCAAGCAAAGGGGGTCAATA 59.923 47.619 0.00 0.00 0.00 1.90
355 381 0.178924 AGCAAGCAAAGGGGGTCAAT 60.179 50.000 0.00 0.00 0.00 2.57
356 382 1.114722 CAGCAAGCAAAGGGGGTCAA 61.115 55.000 0.00 0.00 0.00 3.18
383 414 9.878737 TTATATTAGTTTACAGAGGGAGTAGCT 57.121 33.333 0.00 0.00 0.00 3.32
388 419 8.861086 TGCTCTTATATTAGTTTACAGAGGGAG 58.139 37.037 0.00 0.00 0.00 4.30
439 470 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
440 471 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
441 472 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
442 473 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
443 474 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
444 475 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
445 476 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
446 477 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
447 478 9.646522 AAGTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
448 479 9.289782 GAAGTACTCCCTCCGTAAACTAATATA 57.710 37.037 0.00 0.00 0.00 0.86
449 480 8.003629 AGAAGTACTCCCTCCGTAAACTAATAT 58.996 37.037 0.00 0.00 0.00 1.28
450 481 7.349598 AGAAGTACTCCCTCCGTAAACTAATA 58.650 38.462 0.00 0.00 0.00 0.98
451 482 6.193504 AGAAGTACTCCCTCCGTAAACTAAT 58.806 40.000 0.00 0.00 0.00 1.73
452 483 5.574188 AGAAGTACTCCCTCCGTAAACTAA 58.426 41.667 0.00 0.00 0.00 2.24
453 484 5.184892 AGAAGTACTCCCTCCGTAAACTA 57.815 43.478 0.00 0.00 0.00 2.24
454 485 4.044946 AGAAGTACTCCCTCCGTAAACT 57.955 45.455 0.00 0.00 0.00 2.66
455 486 4.797800 AAGAAGTACTCCCTCCGTAAAC 57.202 45.455 0.00 0.00 0.00 2.01
456 487 5.595952 GGATAAGAAGTACTCCCTCCGTAAA 59.404 44.000 0.00 0.00 0.00 2.01
457 488 5.103771 AGGATAAGAAGTACTCCCTCCGTAA 60.104 44.000 0.00 0.00 0.00 3.18
458 489 4.414846 AGGATAAGAAGTACTCCCTCCGTA 59.585 45.833 0.00 0.00 0.00 4.02
459 490 3.204831 AGGATAAGAAGTACTCCCTCCGT 59.795 47.826 0.00 0.00 0.00 4.69
460 491 3.822167 GAGGATAAGAAGTACTCCCTCCG 59.178 52.174 0.00 0.00 35.53 4.63
461 492 4.140876 AGGAGGATAAGAAGTACTCCCTCC 60.141 50.000 22.48 22.48 46.93 4.30
462 493 5.069518 AGGAGGATAAGAAGTACTCCCTC 57.930 47.826 0.00 5.94 46.93 4.30
463 494 4.482772 TGAGGAGGATAAGAAGTACTCCCT 59.517 45.833 0.00 0.00 46.93 4.20
464 495 4.805744 TGAGGAGGATAAGAAGTACTCCC 58.194 47.826 0.00 0.00 46.93 4.30
465 496 5.182380 CGATGAGGAGGATAAGAAGTACTCC 59.818 48.000 0.00 0.00 46.27 3.85
466 497 5.766174 ACGATGAGGAGGATAAGAAGTACTC 59.234 44.000 0.00 0.00 0.00 2.59
467 498 5.697067 ACGATGAGGAGGATAAGAAGTACT 58.303 41.667 0.00 0.00 0.00 2.73
468 499 5.334260 CGACGATGAGGAGGATAAGAAGTAC 60.334 48.000 0.00 0.00 0.00 2.73
469 500 4.755629 CGACGATGAGGAGGATAAGAAGTA 59.244 45.833 0.00 0.00 0.00 2.24
470 501 3.566322 CGACGATGAGGAGGATAAGAAGT 59.434 47.826 0.00 0.00 0.00 3.01
471 502 3.566322 ACGACGATGAGGAGGATAAGAAG 59.434 47.826 0.00 0.00 0.00 2.85
472 503 3.552875 ACGACGATGAGGAGGATAAGAA 58.447 45.455 0.00 0.00 0.00 2.52
473 504 3.139850 GACGACGATGAGGAGGATAAGA 58.860 50.000 0.00 0.00 0.00 2.10
474 505 2.096169 CGACGACGATGAGGAGGATAAG 60.096 54.545 0.00 0.00 42.66 1.73
475 506 1.871676 CGACGACGATGAGGAGGATAA 59.128 52.381 0.00 0.00 42.66 1.75
476 507 1.509703 CGACGACGATGAGGAGGATA 58.490 55.000 0.00 0.00 42.66 2.59
477 508 1.167155 CCGACGACGATGAGGAGGAT 61.167 60.000 9.28 0.00 42.66 3.24
484 515 1.642037 GAGGTCACCGACGACGATGA 61.642 60.000 9.28 4.10 39.97 2.92
485 516 1.226323 GAGGTCACCGACGACGATG 60.226 63.158 9.28 0.94 42.66 3.84
486 517 2.404995 GGAGGTCACCGACGACGAT 61.405 63.158 9.28 0.00 42.66 3.73
565 596 2.564553 GATCGAGCCGACAAGCTGGT 62.565 60.000 0.00 0.00 45.15 4.00
567 598 1.880340 GGATCGAGCCGACAAGCTG 60.880 63.158 2.80 0.00 45.15 4.24
569 600 1.227380 ATGGATCGAGCCGACAAGC 60.227 57.895 16.16 0.00 39.18 4.01
744 995 4.514577 ATCGCCGGGTCTTGCTCG 62.515 66.667 2.18 0.00 41.64 5.03
748 999 2.202932 CCTGATCGCCGGGTCTTG 60.203 66.667 2.18 0.00 36.52 3.02
771 1022 2.433491 CCGTCGGTCGATGCCAAA 60.433 61.111 2.08 0.00 42.86 3.28
789 1040 2.654912 CCGTCACGTTGCTTCCGTC 61.655 63.158 0.00 0.00 36.17 4.79
867 1118 0.318784 GGAATCGAATCGGGAGACGG 60.319 60.000 1.76 0.00 44.82 4.79
913 1164 4.144703 GGAGGCGACGGGGAAGAC 62.145 72.222 0.00 0.00 0.00 3.01
931 1182 5.278218 GGAGAAAGAAGTCAAAGCTTTGGAG 60.278 44.000 33.01 13.28 38.66 3.86
932 1183 4.580580 GGAGAAAGAAGTCAAAGCTTTGGA 59.419 41.667 33.01 19.76 38.66 3.53
933 1184 4.555511 CGGAGAAAGAAGTCAAAGCTTTGG 60.556 45.833 33.01 18.01 38.66 3.28
934 1185 4.531332 CGGAGAAAGAAGTCAAAGCTTTG 58.469 43.478 29.53 29.53 39.48 2.77
938 1189 2.147150 AGCGGAGAAAGAAGTCAAAGC 58.853 47.619 0.00 0.00 0.00 3.51
1317 1578 3.834799 CCGCGGTGGTAGAGGTCC 61.835 72.222 19.50 0.00 0.00 4.46
1578 1854 2.029739 TCATTTTGCACATCTGTGGCTG 60.030 45.455 11.98 0.71 45.72 4.85
1600 1876 5.220989 GCATATTCAGACTGCACATTGTCAT 60.221 40.000 6.59 0.00 35.96 3.06
1640 1916 9.887629 CCAGATAGATATGTAAATCAAGCAGAT 57.112 33.333 0.00 0.00 39.09 2.90
1643 1919 7.388776 GTGCCAGATAGATATGTAAATCAAGCA 59.611 37.037 0.00 0.00 0.00 3.91
1659 1935 4.202050 GGCCAAAAACTATGTGCCAGATAG 60.202 45.833 7.29 7.29 35.49 2.08
1661 1937 2.497273 GGCCAAAAACTATGTGCCAGAT 59.503 45.455 0.00 0.00 35.49 2.90
1662 1938 1.892474 GGCCAAAAACTATGTGCCAGA 59.108 47.619 0.00 0.00 35.49 3.86
1663 1939 1.066929 GGGCCAAAAACTATGTGCCAG 60.067 52.381 4.39 0.00 36.46 4.85
1664 1940 0.972883 GGGCCAAAAACTATGTGCCA 59.027 50.000 4.39 0.00 36.46 4.92
1665 1941 0.972883 TGGGCCAAAAACTATGTGCC 59.027 50.000 2.13 0.00 35.00 5.01
1687 1963 3.916172 CCAATTCAACATCGTGAGCAAAG 59.084 43.478 0.00 0.00 0.00 2.77
1688 1964 3.305267 CCCAATTCAACATCGTGAGCAAA 60.305 43.478 0.00 0.00 0.00 3.68
1689 1965 2.228582 CCCAATTCAACATCGTGAGCAA 59.771 45.455 0.00 0.00 0.00 3.91
1692 1968 2.679837 CTCCCCAATTCAACATCGTGAG 59.320 50.000 0.00 0.00 0.00 3.51
1693 1969 2.710377 CTCCCCAATTCAACATCGTGA 58.290 47.619 0.00 0.00 0.00 4.35
1695 1971 1.271871 TGCTCCCCAATTCAACATCGT 60.272 47.619 0.00 0.00 0.00 3.73
1696 1972 1.462616 TGCTCCCCAATTCAACATCG 58.537 50.000 0.00 0.00 0.00 3.84
1736 2074 6.477688 TCGAAACAGAAACAGACTAAAACGAT 59.522 34.615 0.00 0.00 0.00 3.73
1739 2077 6.357240 GCATCGAAACAGAAACAGACTAAAAC 59.643 38.462 0.00 0.00 0.00 2.43
1775 2121 7.692705 GGAATTAGCATCTGAAAAACGTAACTC 59.307 37.037 0.00 0.00 0.00 3.01
1841 2188 3.555527 ACAGCATGAGCATATGTCACT 57.444 42.857 4.29 0.00 45.49 3.41
1846 2193 4.097437 ACCTGAAAACAGCATGAGCATATG 59.903 41.667 0.00 0.00 45.49 1.78
1891 2239 6.648725 GCACTATTTCTGATCCTACAATCTCC 59.351 42.308 0.00 0.00 0.00 3.71
1897 2245 4.887655 TCTCGCACTATTTCTGATCCTACA 59.112 41.667 0.00 0.00 0.00 2.74
1969 2317 4.720046 GAAGACAAACCTTCTCCCTTTCT 58.280 43.478 0.00 0.00 39.44 2.52
2032 2384 9.211485 AGGCATTGTGAGAAATTTAAAATTCAG 57.789 29.630 16.37 1.51 0.00 3.02
2203 2744 9.429359 CTACTAATGGATAATGCCTACAGAAAG 57.571 37.037 0.00 0.00 0.00 2.62
2207 2748 8.753133 TGATCTACTAATGGATAATGCCTACAG 58.247 37.037 0.00 0.00 0.00 2.74
2422 2965 4.755411 ACACTACGATGGTGTCTATTTGG 58.245 43.478 0.00 0.00 43.35 3.28
2479 3023 3.753294 AGTAAGTGAACCACAGTGAGG 57.247 47.619 4.89 4.89 36.74 3.86
2489 3033 9.269453 AGTATTACAACAGGAAAGTAAGTGAAC 57.731 33.333 0.00 0.00 31.96 3.18
2516 3060 2.906389 TCTCTAGGACACAACCAGCATT 59.094 45.455 0.00 0.00 0.00 3.56
2552 3096 8.737168 AAATGCAAACTAGAGCTAACATCATA 57.263 30.769 0.00 0.00 0.00 2.15
2794 3338 7.663905 ACTGTCTGGTGCTACAAATTATACAAA 59.336 33.333 0.00 0.00 0.00 2.83
2875 3419 9.961265 GCCACACTTAGTTTTATTCTTTTTACT 57.039 29.630 0.00 0.00 0.00 2.24
2898 3442 2.398252 CTTGAGAAGCTGAGATGCCA 57.602 50.000 0.00 0.00 0.00 4.92
2947 3491 9.234827 TCACAGATTCATTCAATACAAATCAGT 57.765 29.630 0.00 0.00 0.00 3.41
2986 3530 1.610522 CCAAACTTTCCTGCTCCACAG 59.389 52.381 0.00 0.00 46.77 3.66
3174 3718 6.615088 ACTTGCATTGTACAACATCATTCTC 58.385 36.000 11.22 0.00 0.00 2.87
3209 3753 8.621532 AAGATTTTGCAAGTTCTCTGTATGTA 57.378 30.769 12.11 0.00 0.00 2.29
3286 3830 8.354711 TGCTGGTCCAAACATTTAATATGTTA 57.645 30.769 13.04 1.09 40.94 2.41
3316 3860 7.919690 TCCATTCATTTGTAAAGCTAGAATCG 58.080 34.615 0.00 0.00 0.00 3.34
3504 4057 9.561069 TCATTTATAAACTAGAATCCCTTCTGC 57.439 33.333 0.00 0.00 41.83 4.26
3533 4091 3.197983 AGGTATCCTTCCAATGGGTTCA 58.802 45.455 0.00 0.00 34.93 3.18
3554 4112 9.567776 TGACATGAAACTGTTCTAAAGGATTTA 57.432 29.630 0.00 0.00 40.09 1.40
3567 4130 4.281435 TGCCATTGATTGACATGAAACTGT 59.719 37.500 0.00 0.00 0.00 3.55
3620 4183 5.302059 GGATATATAGCAGATCGCACCCTTA 59.698 44.000 11.20 0.00 46.13 2.69
3621 4184 4.100189 GGATATATAGCAGATCGCACCCTT 59.900 45.833 11.20 0.00 46.13 3.95
3664 4227 3.897505 TCAAGCATATACTAGCAGCTCCA 59.102 43.478 0.00 0.00 33.83 3.86
3665 4228 4.527509 TCAAGCATATACTAGCAGCTCC 57.472 45.455 0.00 0.00 33.83 4.70
3670 4233 7.066307 TCAGGAATTCAAGCATATACTAGCA 57.934 36.000 7.93 0.00 0.00 3.49
3811 4374 2.717044 CGCGTCCCCATCAGGTACA 61.717 63.158 0.00 0.00 0.00 2.90
3829 4392 0.255890 TGTAGGAAGAGCCATTGCCC 59.744 55.000 0.00 0.00 40.02 5.36
3878 4441 2.278596 CACATAGTCGGACGGCGG 60.279 66.667 13.24 0.00 0.00 6.13
3901 4464 1.007154 TGCCGATCGACACGAACAA 60.007 52.632 18.66 0.00 39.99 2.83
4069 4633 4.397348 ACGCAAACAGGGTCATCC 57.603 55.556 0.00 0.00 39.51 3.51
4081 4645 2.344500 CGGTAAGGTGGGACGCAA 59.656 61.111 0.00 0.00 43.02 4.85


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

AutoCloner maintained by Alex Coulton.