Multiple sequence alignment - TraesCS2B01G511000

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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 TraesCS2B01G511000 chr2B 100.000 2724 0 0 1 2724 706790895 706788172 0.000000e+00 5031.0
1 TraesCS2B01G511000 chr2B 85.865 1705 200 24 46 1728 758898313 758899998 0.000000e+00 1775.0
2 TraesCS2B01G511000 chr2B 78.223 349 52 9 1585 1909 706920915 706920567 4.600000e-48 202.0
3 TraesCS2B01G511000 chr2B 77.485 342 53 9 1592 1909 706729301 706728960 1.670000e-42 183.0
4 TraesCS2B01G511000 chr2B 74.545 440 87 22 871 1300 707656576 707656152 4.660000e-38 169.0
5 TraesCS2B01G511000 chr2B 79.412 136 21 5 1188 1321 707518531 707518401 3.740000e-14 89.8
6 TraesCS2B01G511000 chr2D 85.277 2581 263 59 57 2575 585694293 585691768 0.000000e+00 2553.0
7 TraesCS2B01G511000 chr2D 85.815 1699 210 22 46 1728 619575040 619576723 0.000000e+00 1773.0
8 TraesCS2B01G511000 chr2D 82.993 1029 135 17 88 1108 585738381 585737385 0.000000e+00 894.0
9 TraesCS2B01G511000 chr2D 77.205 737 95 34 1199 1909 585684953 585684264 1.990000e-96 363.0
10 TraesCS2B01G511000 chr2A 85.575 2149 246 30 87 2203 719737820 719735704 0.000000e+00 2193.0
11 TraesCS2B01G511000 chr2A 83.827 1756 232 30 1 1724 751173299 751175034 0.000000e+00 1622.0
12 TraesCS2B01G511000 chr2A 86.016 1373 153 24 7 1375 751014987 751016324 0.000000e+00 1435.0
13 TraesCS2B01G511000 chr2A 85.868 1302 144 24 77 1375 751048515 751049779 0.000000e+00 1349.0
14 TraesCS2B01G511000 chr2A 87.785 745 78 9 393 1133 751055338 751056073 0.000000e+00 859.0
15 TraesCS2B01G511000 chr2A 78.444 617 114 12 1126 1728 751056917 751057528 4.250000e-103 385.0
16 TraesCS2B01G511000 chr6B 75.737 441 87 16 870 1304 698990319 698990745 1.280000e-48 204.0


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 TraesCS2B01G511000 chr2B 706788172 706790895 2723 True 5031 5031 100.0000 1 2724 1 chr2B.!!$R2 2723
1 TraesCS2B01G511000 chr2B 758898313 758899998 1685 False 1775 1775 85.8650 46 1728 1 chr2B.!!$F1 1682
2 TraesCS2B01G511000 chr2D 585691768 585694293 2525 True 2553 2553 85.2770 57 2575 1 chr2D.!!$R2 2518
3 TraesCS2B01G511000 chr2D 619575040 619576723 1683 False 1773 1773 85.8150 46 1728 1 chr2D.!!$F1 1682
4 TraesCS2B01G511000 chr2D 585737385 585738381 996 True 894 894 82.9930 88 1108 1 chr2D.!!$R3 1020
5 TraesCS2B01G511000 chr2D 585684264 585684953 689 True 363 363 77.2050 1199 1909 1 chr2D.!!$R1 710
6 TraesCS2B01G511000 chr2A 719735704 719737820 2116 True 2193 2193 85.5750 87 2203 1 chr2A.!!$R1 2116
7 TraesCS2B01G511000 chr2A 751173299 751175034 1735 False 1622 1622 83.8270 1 1724 1 chr2A.!!$F3 1723
8 TraesCS2B01G511000 chr2A 751014987 751016324 1337 False 1435 1435 86.0160 7 1375 1 chr2A.!!$F1 1368
9 TraesCS2B01G511000 chr2A 751048515 751049779 1264 False 1349 1349 85.8680 77 1375 1 chr2A.!!$F2 1298
10 TraesCS2B01G511000 chr2A 751055338 751057528 2190 False 622 859 83.1145 393 1728 2 chr2A.!!$F4 1335

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
147 162 0.325933 TCCCAGTCATGGCAAGTCTG 59.674 55.0 9.49 9.49 46.19 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 3026 0.102481 ATTACGACCCGCACAGCTAG 59.898 55.0 0.0 0.0 0.0 3.42 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 28 8.980481 TCTCCTTCCACCTAAATCAATATTTC 57.020 34.615 0.00 0.00 36.67 2.17
35 37 6.207417 ACCTAAATCAATATTTCGCCTGGATG 59.793 38.462 0.00 0.00 36.67 3.51
47 49 2.009042 GCCTGGATGTACACAGTGCTC 61.009 57.143 11.36 0.00 32.90 4.26
104 119 5.822519 TGTTGTCTTTTGCAGTCAGTAAGAT 59.177 36.000 0.00 0.00 31.76 2.40
117 132 3.056536 TCAGTAAGATGACAGGTGCACTC 60.057 47.826 17.98 7.24 0.00 3.51
147 162 0.325933 TCCCAGTCATGGCAAGTCTG 59.674 55.000 9.49 9.49 46.19 3.51
200 215 1.063806 CGCAAGTCGAGAGGTTGAAG 58.936 55.000 0.00 0.00 41.67 3.02
209 224 3.506455 TCGAGAGGTTGAAGAAGATTCGT 59.494 43.478 0.00 0.00 0.00 3.85
281 305 2.603075 TTAATTCCTGGCAGGCAAGT 57.397 45.000 29.02 22.31 34.61 3.16
286 310 1.207488 TCCTGGCAGGCAAGTACCAT 61.207 55.000 29.02 0.00 34.61 3.55
317 341 3.327172 ACCCATGAATTTTGTGATGCCAA 59.673 39.130 0.00 0.00 0.00 4.52
334 358 2.802247 GCCAAAACAACTGAGCAATTCC 59.198 45.455 0.00 0.00 0.00 3.01
389 414 4.260170 GTGGATCAGCTTCAAAGACATCT 58.740 43.478 0.00 0.00 0.00 2.90
402 427 3.054802 AAAGACATCTTCCCTGCTACAGG 60.055 47.826 6.65 6.65 42.25 4.00
493 519 6.929049 TCCACTTTGACAATTACAGTAGTGAG 59.071 38.462 13.14 6.05 35.65 3.51
495 521 7.604164 CCACTTTGACAATTACAGTAGTGAGAT 59.396 37.037 13.14 0.00 35.65 2.75
512 538 6.686130 GTGAGATGCACTTTTTCATTTCTG 57.314 37.500 0.00 0.00 44.27 3.02
513 539 5.118203 GTGAGATGCACTTTTTCATTTCTGC 59.882 40.000 0.00 0.00 44.27 4.26
514 540 4.232221 AGATGCACTTTTTCATTTCTGCG 58.768 39.130 0.00 0.00 0.00 5.18
515 541 2.741612 TGCACTTTTTCATTTCTGCGG 58.258 42.857 0.00 0.00 0.00 5.69
528 554 8.675705 TTCATTTCTGCGGATTAATCTGAATA 57.324 30.769 25.44 7.32 35.13 1.75
531 557 9.903682 CATTTCTGCGGATTAATCTGAATAATT 57.096 29.630 25.44 9.50 35.13 1.40
545 571 3.118186 TGAATAATTCCACCACGTAGGGG 60.118 47.826 0.00 0.00 43.89 4.79
689 715 8.923683 GTTAGACTTCTTGGTTACTGTATTCAC 58.076 37.037 0.00 0.00 0.00 3.18
753 779 7.556635 ACAAAAGCTTAGACTACTTCCTGTTTT 59.443 33.333 0.00 0.00 0.00 2.43
759 785 7.817962 GCTTAGACTACTTCCTGTTTTGTATGA 59.182 37.037 0.00 0.00 0.00 2.15
760 786 9.706691 CTTAGACTACTTCCTGTTTTGTATGAA 57.293 33.333 0.00 0.00 0.00 2.57
923 950 4.016851 TCAAAGGGGTAGCTAGAGGACTTA 60.017 45.833 0.00 0.00 0.00 2.24
987 1015 5.942236 AGATCTCAAAGCAAGCAACATCTTA 59.058 36.000 0.00 0.00 0.00 2.10
1017 1045 4.752101 GTGGAGATGAGACCCAAAATATCG 59.248 45.833 0.00 0.00 0.00 2.92
1038 1066 3.118665 CGGATTTTGGAATGGCAAGGATT 60.119 43.478 0.00 0.00 0.00 3.01
1047 1075 4.323715 GGAATGGCAAGGATTTTTGGTGAT 60.324 41.667 0.00 0.00 0.00 3.06
1115 1149 5.817784 AGTAGTAACTCCTGCACTCTAGAA 58.182 41.667 0.00 0.00 0.00 2.10
1165 2053 5.825507 AGCTTCAACTCATCAGTTTTTGTC 58.174 37.500 0.00 0.00 41.24 3.18
1307 2195 0.931005 GGTTAAAGATCAGCTCGCCG 59.069 55.000 0.00 0.00 0.00 6.46
1321 2221 2.688507 CTCGCCGCATCACCTTATAAT 58.311 47.619 0.00 0.00 0.00 1.28
1368 2273 3.636300 TGTAAGTGTTGCCAAATGCTTCT 59.364 39.130 0.00 0.00 42.00 2.85
1426 2338 5.106712 TGTTTATGAATGCTCGACCTTGTTC 60.107 40.000 0.00 0.00 0.00 3.18
1461 2373 4.634012 TCCTGAAAGAAGGAAAATCCGA 57.366 40.909 0.00 0.00 43.57 4.55
1485 2397 3.402628 TTTCCTAGACACAGTGCTTCC 57.597 47.619 0.00 0.00 0.00 3.46
1487 2399 0.108615 CCTAGACACAGTGCTTCCGG 60.109 60.000 0.00 0.00 0.00 5.14
1535 2447 2.295349 CTGTGCATCCATATTGGCCTTC 59.705 50.000 3.32 0.00 37.47 3.46
1659 2571 2.106683 CCGTCGGGAGGAAACATGC 61.107 63.158 2.34 0.00 34.06 4.06
1687 2599 2.301583 AGAAGCAAGGGAGAACTCTGTC 59.698 50.000 1.86 0.00 0.00 3.51
1693 2605 4.392940 CAAGGGAGAACTCTGTCAACAAT 58.607 43.478 1.86 0.00 0.00 2.71
1797 2728 0.755327 GCCAAGTGGGTTTCAGTGGT 60.755 55.000 0.00 0.00 39.65 4.16
1854 2790 3.522553 CCCTCGTCTGATGGTTAGTTTC 58.477 50.000 0.00 0.00 0.00 2.78
1953 2889 0.915872 ACTGCTGGGATCCATGACCA 60.916 55.000 15.23 0.29 30.82 4.02
1959 2895 3.368248 CTGGGATCCATGACCATTTTGT 58.632 45.455 15.23 0.00 33.07 2.83
1990 2926 3.092301 CAAAAGGGAGGGAAATGAGGTC 58.908 50.000 0.00 0.00 0.00 3.85
1991 2927 2.059756 AAGGGAGGGAAATGAGGTCA 57.940 50.000 0.00 0.00 0.00 4.02
2102 3038 2.257353 AAAAAGCTAGCTGTGCGGG 58.743 52.632 20.16 0.00 35.28 6.13
2163 3101 4.382362 GCCTAAGAGGGTACGTGTACAAAT 60.382 45.833 11.89 0.00 37.78 2.32
2187 3127 0.109132 CGTGAGAAAAGGGCAATGGC 60.109 55.000 0.00 0.00 40.13 4.40
2203 3143 4.677779 GCAATGGCGATTGTGAAAACCTAT 60.678 41.667 20.66 0.00 41.09 2.57
2205 3145 3.950397 TGGCGATTGTGAAAACCTATCT 58.050 40.909 0.00 0.00 0.00 1.98
2206 3146 3.689161 TGGCGATTGTGAAAACCTATCTG 59.311 43.478 0.00 0.00 0.00 2.90
2211 3151 2.972625 TGTGAAAACCTATCTGCCTCG 58.027 47.619 0.00 0.00 0.00 4.63
2234 3174 2.736826 GCCTTCCCTTCTAGCCGCT 61.737 63.158 0.00 0.00 0.00 5.52
2300 3240 1.272807 CTGGGAGGTCCGTTTAAGGA 58.727 55.000 0.00 0.00 38.76 3.36
2307 3247 2.041216 AGGTCCGTTTAAGGATGGCTTT 59.959 45.455 0.00 0.00 43.04 3.51
2310 3250 3.127030 GTCCGTTTAAGGATGGCTTTCTG 59.873 47.826 0.00 0.00 43.04 3.02
2312 3252 2.423538 CGTTTAAGGATGGCTTTCTGGG 59.576 50.000 0.00 0.00 0.00 4.45
2323 3265 1.539157 CTTTCTGGGAAGTTGGAGGC 58.461 55.000 0.00 0.00 0.00 4.70
2331 3273 0.693049 GAAGTTGGAGGCCTTGGAGA 59.307 55.000 6.77 0.00 0.00 3.71
2333 3275 1.377856 GTTGGAGGCCTTGGAGAGC 60.378 63.158 6.77 0.00 0.00 4.09
2356 3298 2.302260 CTGCGGTCAGAGAAGGAGATA 58.698 52.381 0.00 0.00 42.95 1.98
2395 3337 2.581354 GTCAGGTCATGCTCGGCT 59.419 61.111 0.00 0.00 0.00 5.52
2433 3375 3.000819 AGTGGCCGGACGAATCCA 61.001 61.111 5.05 0.00 46.67 3.41
2437 3379 2.264794 GCCGGACGAATCCAGTGT 59.735 61.111 5.05 0.00 46.67 3.55
2481 3423 3.550974 GCCTAGGCCATCGGAGAA 58.449 61.111 24.19 0.00 35.69 2.87
2486 3428 1.202582 CTAGGCCATCGGAGAATACGG 59.797 57.143 5.01 0.00 43.58 4.02
2488 3430 1.668151 GCCATCGGAGAATACGGCC 60.668 63.158 0.00 0.00 43.58 6.13
2489 3431 1.372997 CCATCGGAGAATACGGCCG 60.373 63.158 26.86 26.86 43.58 6.13
2490 3432 1.372997 CATCGGAGAATACGGCCGG 60.373 63.158 31.76 11.88 43.58 6.13
2492 3434 2.989173 ATCGGAGAATACGGCCGGGA 62.989 60.000 31.76 18.02 43.58 5.14
2493 3435 2.420466 GGAGAATACGGCCGGGAC 59.580 66.667 31.76 17.20 0.00 4.46
2509 3465 1.131126 GGGACGACAACGAGTTCGATA 59.869 52.381 8.72 0.00 43.02 2.92
2515 3471 4.142752 ACGACAACGAGTTCGATATCAGAA 60.143 41.667 8.72 4.89 43.02 3.02
2531 3487 0.038526 AGAACTGGACTTGGCGTACG 60.039 55.000 11.84 11.84 0.00 3.67
2537 3493 1.666872 GACTTGGCGTACGTTGGCT 60.667 57.895 17.90 0.00 0.00 4.75
2541 3497 3.428282 GGCGTACGTTGGCTTGGG 61.428 66.667 17.90 0.00 0.00 4.12
2553 3509 3.243359 TGGCTTGGGAAATTTGTCTCT 57.757 42.857 0.00 0.00 0.00 3.10
2566 3522 2.185004 TGTCTCTGGTTGCCTTTAGC 57.815 50.000 0.00 0.00 44.14 3.09
2575 3531 3.271729 GGTTGCCTTTAGCTAGTCTTCC 58.728 50.000 0.00 0.00 44.23 3.46
2576 3532 3.271729 GTTGCCTTTAGCTAGTCTTCCC 58.728 50.000 0.00 0.00 44.23 3.97
2577 3533 2.834113 TGCCTTTAGCTAGTCTTCCCT 58.166 47.619 0.00 0.00 44.23 4.20
2578 3534 3.990369 TGCCTTTAGCTAGTCTTCCCTA 58.010 45.455 0.00 0.00 44.23 3.53
2579 3535 3.705072 TGCCTTTAGCTAGTCTTCCCTAC 59.295 47.826 0.00 0.00 44.23 3.18
2580 3536 3.962063 GCCTTTAGCTAGTCTTCCCTACT 59.038 47.826 0.00 0.00 38.99 2.57
2581 3537 4.202172 GCCTTTAGCTAGTCTTCCCTACTG 60.202 50.000 0.00 0.00 38.99 2.74
2582 3538 4.342665 CCTTTAGCTAGTCTTCCCTACTGG 59.657 50.000 0.00 0.00 0.00 4.00
2583 3539 4.604784 TTAGCTAGTCTTCCCTACTGGT 57.395 45.455 0.00 0.00 34.77 4.00
2584 3540 5.722172 TTAGCTAGTCTTCCCTACTGGTA 57.278 43.478 0.00 0.00 34.77 3.25
2585 3541 4.817874 AGCTAGTCTTCCCTACTGGTAT 57.182 45.455 0.00 0.00 34.77 2.73
2586 3542 4.732065 AGCTAGTCTTCCCTACTGGTATC 58.268 47.826 0.00 0.00 34.77 2.24
2587 3543 4.168283 AGCTAGTCTTCCCTACTGGTATCA 59.832 45.833 0.00 0.00 34.77 2.15
2588 3544 4.521256 GCTAGTCTTCCCTACTGGTATCAG 59.479 50.000 0.04 0.04 46.10 2.90
2598 3554 1.671979 CTGGTATCAGTGGTGGCATG 58.328 55.000 0.00 0.00 36.30 4.06
2599 3555 1.210234 CTGGTATCAGTGGTGGCATGA 59.790 52.381 0.00 0.00 36.30 3.07
2600 3556 1.845791 TGGTATCAGTGGTGGCATGAT 59.154 47.619 0.00 6.56 37.44 2.45
2601 3557 2.158769 TGGTATCAGTGGTGGCATGATC 60.159 50.000 4.67 0.00 35.39 2.92
2602 3558 2.158769 GGTATCAGTGGTGGCATGATCA 60.159 50.000 4.67 0.00 35.39 2.92
2603 3559 2.048444 ATCAGTGGTGGCATGATCAC 57.952 50.000 0.00 3.84 34.61 3.06
2604 3560 0.986527 TCAGTGGTGGCATGATCACT 59.013 50.000 15.83 6.97 40.62 3.41
2605 3561 1.352017 TCAGTGGTGGCATGATCACTT 59.648 47.619 15.83 3.97 38.27 3.16
2606 3562 1.741706 CAGTGGTGGCATGATCACTTC 59.258 52.381 15.83 10.72 38.27 3.01
2607 3563 1.352017 AGTGGTGGCATGATCACTTCA 59.648 47.619 15.83 6.91 37.18 3.02
2608 3564 2.161855 GTGGTGGCATGATCACTTCAA 58.838 47.619 15.83 2.14 38.03 2.69
2609 3565 2.557924 GTGGTGGCATGATCACTTCAAA 59.442 45.455 15.83 0.00 38.03 2.69
2610 3566 3.194116 GTGGTGGCATGATCACTTCAAAT 59.806 43.478 15.83 0.00 38.03 2.32
2611 3567 3.833650 TGGTGGCATGATCACTTCAAATT 59.166 39.130 15.83 0.00 38.03 1.82
2612 3568 4.178540 GGTGGCATGATCACTTCAAATTG 58.821 43.478 15.83 0.00 38.03 2.32
2613 3569 4.178540 GTGGCATGATCACTTCAAATTGG 58.821 43.478 0.00 0.00 38.03 3.16
2614 3570 4.082081 GTGGCATGATCACTTCAAATTGGA 60.082 41.667 0.00 0.00 38.03 3.53
2615 3571 4.158949 TGGCATGATCACTTCAAATTGGAG 59.841 41.667 0.00 0.00 38.03 3.86
2616 3572 4.441079 GGCATGATCACTTCAAATTGGAGG 60.441 45.833 6.21 0.00 38.03 4.30
2617 3573 4.441079 GCATGATCACTTCAAATTGGAGGG 60.441 45.833 6.21 0.97 38.03 4.30
2618 3574 4.656100 TGATCACTTCAAATTGGAGGGA 57.344 40.909 8.92 8.92 0.00 4.20
2619 3575 4.335416 TGATCACTTCAAATTGGAGGGAC 58.665 43.478 8.64 4.01 0.00 4.46
2620 3576 3.874383 TCACTTCAAATTGGAGGGACA 57.126 42.857 1.26 0.00 0.00 4.02
2621 3577 4.177537 TCACTTCAAATTGGAGGGACAA 57.822 40.909 1.26 0.00 34.41 3.18
2622 3578 4.739793 TCACTTCAAATTGGAGGGACAAT 58.260 39.130 1.26 0.00 42.56 2.71
2627 3583 1.571955 AATTGGAGGGACAATTGGGC 58.428 50.000 10.83 1.05 46.23 5.36
2628 3584 0.325577 ATTGGAGGGACAATTGGGCC 60.326 55.000 10.83 10.50 37.81 5.80
2629 3585 1.734420 TTGGAGGGACAATTGGGCCA 61.734 55.000 17.91 0.00 0.00 5.36
2630 3586 1.078347 GGAGGGACAATTGGGCCAA 59.922 57.895 23.33 23.33 0.00 4.52
2631 3587 0.544120 GGAGGGACAATTGGGCCAAA 60.544 55.000 24.97 0.00 0.00 3.28
2632 3588 1.571955 GAGGGACAATTGGGCCAAAT 58.428 50.000 24.97 13.01 0.00 2.32
2633 3589 1.908619 GAGGGACAATTGGGCCAAATT 59.091 47.619 24.97 12.72 0.00 1.82
2634 3590 1.908619 AGGGACAATTGGGCCAAATTC 59.091 47.619 24.97 18.27 0.00 2.17
2635 3591 1.065491 GGGACAATTGGGCCAAATTCC 60.065 52.381 24.97 25.24 0.00 3.01
2636 3592 1.065491 GGACAATTGGGCCAAATTCCC 60.065 52.381 24.97 17.71 44.17 3.97
2643 3599 2.159179 GGGCCAAATTCCCATACTGT 57.841 50.000 4.39 0.00 43.37 3.55
2644 3600 3.306472 GGGCCAAATTCCCATACTGTA 57.694 47.619 4.39 0.00 43.37 2.74
2645 3601 3.637769 GGGCCAAATTCCCATACTGTAA 58.362 45.455 4.39 0.00 43.37 2.41
2646 3602 4.027437 GGGCCAAATTCCCATACTGTAAA 58.973 43.478 4.39 0.00 43.37 2.01
2647 3603 4.468153 GGGCCAAATTCCCATACTGTAAAA 59.532 41.667 4.39 0.00 43.37 1.52
2648 3604 5.046231 GGGCCAAATTCCCATACTGTAAAAA 60.046 40.000 4.39 0.00 43.37 1.94
2696 3652 2.019984 GCTATCTGCTTTTCCACTGGG 58.980 52.381 0.00 0.00 38.95 4.45
2697 3653 2.619074 GCTATCTGCTTTTCCACTGGGT 60.619 50.000 0.00 0.00 38.95 4.51
2698 3654 1.915141 ATCTGCTTTTCCACTGGGTG 58.085 50.000 0.00 0.00 34.93 4.61
2707 3663 4.850193 CACTGGGTGGGATTGCTT 57.150 55.556 0.00 0.00 0.00 3.91
2708 3664 3.976704 CACTGGGTGGGATTGCTTA 57.023 52.632 0.00 0.00 0.00 3.09
2709 3665 2.214376 CACTGGGTGGGATTGCTTAA 57.786 50.000 0.00 0.00 0.00 1.85
2710 3666 2.094675 CACTGGGTGGGATTGCTTAAG 58.905 52.381 0.00 0.00 0.00 1.85
2711 3667 1.106285 CTGGGTGGGATTGCTTAAGC 58.894 55.000 20.84 20.84 42.50 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 19 4.814234 GTGTACATCCAGGCGAAATATTGA 59.186 41.667 0.00 0.00 0.00 2.57
23 25 1.346395 ACTGTGTACATCCAGGCGAAA 59.654 47.619 15.62 0.00 32.90 3.46
26 28 1.361668 GCACTGTGTACATCCAGGCG 61.362 60.000 15.62 8.80 32.90 5.52
35 37 4.457834 AGTAGATTGGAGCACTGTGTAC 57.542 45.455 9.86 3.96 0.00 2.90
104 119 2.497138 CAATCTTGAGTGCACCTGTCA 58.503 47.619 14.63 8.31 0.00 3.58
108 123 3.731716 TGCAATCTTGAGTGCACCT 57.268 47.368 19.57 0.04 45.52 4.00
117 132 2.189594 TGACTGGGAGTGCAATCTTG 57.810 50.000 14.60 7.03 0.00 3.02
147 162 4.083110 AGACAAATGCACACAAGTATCAGC 60.083 41.667 0.00 0.00 0.00 4.26
281 305 2.131854 CATGGGTCCCTTGGTATGGTA 58.868 52.381 14.88 0.00 0.00 3.25
286 310 4.093011 CAAAATTCATGGGTCCCTTGGTA 58.907 43.478 20.87 11.58 30.78 3.25
317 341 3.820467 TCATCGGAATTGCTCAGTTGTTT 59.180 39.130 0.00 0.00 0.00 2.83
334 358 9.852091 TCTGAATTCTCATCATATAGTTCATCG 57.148 33.333 7.05 0.00 0.00 3.84
402 427 3.499918 CACATTGGAGTCAGAGAAACCAC 59.500 47.826 0.00 0.00 0.00 4.16
469 495 6.929049 TCTCACTACTGTAATTGTCAAAGTGG 59.071 38.462 17.30 4.78 33.52 4.00
493 519 3.365820 CCGCAGAAATGAAAAAGTGCATC 59.634 43.478 0.00 0.00 0.00 3.91
495 521 2.360483 TCCGCAGAAATGAAAAAGTGCA 59.640 40.909 0.00 0.00 0.00 4.57
501 527 7.389803 TCAGATTAATCCGCAGAAATGAAAA 57.610 32.000 11.92 0.00 0.00 2.29
509 535 7.173218 GTGGAATTATTCAGATTAATCCGCAGA 59.827 37.037 11.92 3.04 0.00 4.26
510 536 7.301054 GTGGAATTATTCAGATTAATCCGCAG 58.699 38.462 11.92 0.72 0.00 5.18
511 537 6.206634 GGTGGAATTATTCAGATTAATCCGCA 59.793 38.462 11.92 0.00 0.00 5.69
512 538 6.206634 TGGTGGAATTATTCAGATTAATCCGC 59.793 38.462 11.92 0.98 0.00 5.54
513 539 7.571244 CGTGGTGGAATTATTCAGATTAATCCG 60.571 40.741 11.92 1.83 0.00 4.18
514 540 7.228706 ACGTGGTGGAATTATTCAGATTAATCC 59.771 37.037 11.92 0.00 0.00 3.01
515 541 8.154649 ACGTGGTGGAATTATTCAGATTAATC 57.845 34.615 7.41 7.41 0.00 1.75
528 554 0.616891 GTCCCCTACGTGGTGGAATT 59.383 55.000 4.37 0.00 37.07 2.17
531 557 1.909781 GTGTCCCCTACGTGGTGGA 60.910 63.158 0.00 0.00 34.28 4.02
545 571 0.890996 CCTTGCCACCTTCCAGTGTC 60.891 60.000 0.00 0.00 35.93 3.67
617 643 8.994429 TTGAGATGAGAACTACTTCATTTCTC 57.006 34.615 4.02 4.02 43.75 2.87
639 665 2.754552 AGTTTCTGTGCTGCACTTTTGA 59.245 40.909 30.43 19.98 35.11 2.69
645 671 3.971032 AACTAAGTTTCTGTGCTGCAC 57.029 42.857 25.15 25.15 34.56 4.57
772 798 9.894783 CTCCTATTCTAAATGCAAGAATCATTG 57.105 33.333 13.99 5.56 41.61 2.82
785 811 5.573380 TCAGGCATGCTCCTATTCTAAAT 57.427 39.130 18.92 0.00 33.95 1.40
788 814 3.906218 ACATCAGGCATGCTCCTATTCTA 59.094 43.478 18.92 0.00 35.65 2.10
793 819 3.711190 TCTTAACATCAGGCATGCTCCTA 59.289 43.478 18.92 1.15 35.65 2.94
866 893 2.101783 TGTTGGCCAATCAAGCATAGG 58.898 47.619 23.66 0.00 0.00 2.57
923 950 4.474651 TCTTGAATCATGGTGGAGGTACAT 59.525 41.667 0.00 0.00 0.00 2.29
987 1015 2.441001 GGGTCTCATCTCCACATCCAAT 59.559 50.000 0.00 0.00 0.00 3.16
1017 1045 4.492494 AATCCTTGCCATTCCAAAATCC 57.508 40.909 0.00 0.00 0.00 3.01
1026 1054 4.914177 ATCACCAAAAATCCTTGCCATT 57.086 36.364 0.00 0.00 0.00 3.16
1047 1075 3.670625 AGTATTCGCTTGTTGCTGGTTA 58.329 40.909 0.00 0.00 40.11 2.85
1062 1090 3.131396 CCCGACAACATGCCTAGTATTC 58.869 50.000 0.00 0.00 0.00 1.75
1142 2029 5.221126 GGACAAAAACTGATGAGTTGAAGCT 60.221 40.000 0.00 0.00 41.87 3.74
1152 2039 4.311816 AGCAAGTGGACAAAAACTGATG 57.688 40.909 0.00 0.00 0.00 3.07
1155 2042 3.613737 CACAAGCAAGTGGACAAAAACTG 59.386 43.478 0.97 0.00 35.88 3.16
1157 2044 3.843999 TCACAAGCAAGTGGACAAAAAC 58.156 40.909 8.43 0.00 39.93 2.43
1158 2045 4.527509 TTCACAAGCAAGTGGACAAAAA 57.472 36.364 8.43 0.00 39.93 1.94
1165 2053 3.243035 TGAATCGTTTCACAAGCAAGTGG 60.243 43.478 4.80 0.00 36.94 4.00
1307 2195 7.288810 TGGAAAATCCATTATAAGGTGATGC 57.711 36.000 0.00 0.00 42.67 3.91
1413 2325 2.035442 GCCTGGAACAAGGTCGAGC 61.035 63.158 6.48 6.48 38.70 5.03
1426 2338 0.329261 TCAGGAAGTTCCATGCCTGG 59.671 55.000 23.87 0.78 46.14 4.45
1485 2397 2.508887 GCAGTGAGCAGCTCTCCG 60.509 66.667 23.15 13.12 44.79 4.63
1535 2447 0.886490 GGGCAGTCTTGGACACACAG 60.886 60.000 0.52 0.00 34.60 3.66
1659 2571 1.002888 TCTCCCTTGCTTCTTCTGCAG 59.997 52.381 7.63 7.63 41.71 4.41
1687 2599 0.592637 TCGTCAGGCTTGCATTGTTG 59.407 50.000 0.00 0.00 0.00 3.33
1693 2605 2.819117 CTAGCGTCGTCAGGCTTGCA 62.819 60.000 0.00 0.00 41.03 4.08
1797 2728 0.251354 GATTCTCCACCTGCAGCTGA 59.749 55.000 20.43 2.98 0.00 4.26
1953 2889 4.202010 CCCTTTTGACACGTCTGACAAAAT 60.202 41.667 13.60 0.00 45.03 1.82
1959 2895 1.070134 CCTCCCTTTTGACACGTCTGA 59.930 52.381 0.00 0.00 0.00 3.27
1961 2897 0.396811 CCCTCCCTTTTGACACGTCT 59.603 55.000 0.00 0.00 0.00 4.18
2089 3025 2.552585 TTACGACCCGCACAGCTAGC 62.553 60.000 6.62 6.62 0.00 3.42
2090 3026 0.102481 ATTACGACCCGCACAGCTAG 59.898 55.000 0.00 0.00 0.00 3.42
2091 3027 1.391577 TATTACGACCCGCACAGCTA 58.608 50.000 0.00 0.00 0.00 3.32
2092 3028 0.533491 TTATTACGACCCGCACAGCT 59.467 50.000 0.00 0.00 0.00 4.24
2093 3029 1.578583 ATTATTACGACCCGCACAGC 58.421 50.000 0.00 0.00 0.00 4.40
2094 3030 4.609691 AAAATTATTACGACCCGCACAG 57.390 40.909 0.00 0.00 0.00 3.66
2127 3065 7.489239 ACCCTCTTAGGCAATAGAGATTATC 57.511 40.000 10.83 0.00 40.24 1.75
2163 3101 0.179032 TGCCCTTTTCTCACGAAGCA 60.179 50.000 0.00 0.00 0.00 3.91
2184 3124 3.689161 CAGATAGGTTTTCACAATCGCCA 59.311 43.478 0.00 0.00 0.00 5.69
2187 3127 3.941483 AGGCAGATAGGTTTTCACAATCG 59.059 43.478 0.00 0.00 0.00 3.34
2211 3151 1.443828 CTAGAAGGGAAGGCGGCTC 59.556 63.158 13.70 5.88 0.00 4.70
2255 3195 4.025401 GACACCGTGCGGGCTTTG 62.025 66.667 15.44 6.50 40.62 2.77
2278 3218 2.175035 TTAAACGGACCTCCCAGCGG 62.175 60.000 0.00 0.00 34.14 5.52
2279 3219 0.739813 CTTAAACGGACCTCCCAGCG 60.740 60.000 0.00 0.00 34.14 5.18
2280 3220 0.392595 CCTTAAACGGACCTCCCAGC 60.393 60.000 0.00 0.00 34.14 4.85
2281 3221 1.272807 TCCTTAAACGGACCTCCCAG 58.727 55.000 0.00 0.00 34.14 4.45
2282 3222 1.557832 CATCCTTAAACGGACCTCCCA 59.442 52.381 0.00 0.00 35.52 4.37
2283 3223 1.134189 CCATCCTTAAACGGACCTCCC 60.134 57.143 0.00 0.00 35.52 4.30
2284 3224 1.746171 GCCATCCTTAAACGGACCTCC 60.746 57.143 0.00 0.00 35.52 4.30
2285 3225 1.209747 AGCCATCCTTAAACGGACCTC 59.790 52.381 0.00 0.00 35.52 3.85
2286 3226 1.286248 AGCCATCCTTAAACGGACCT 58.714 50.000 0.00 0.00 35.52 3.85
2287 3227 2.124277 AAGCCATCCTTAAACGGACC 57.876 50.000 0.00 0.00 35.52 4.46
2288 3228 3.127030 CAGAAAGCCATCCTTAAACGGAC 59.873 47.826 0.00 0.00 35.52 4.79
2289 3229 3.343617 CAGAAAGCCATCCTTAAACGGA 58.656 45.455 0.00 0.00 37.50 4.69
2290 3230 2.423538 CCAGAAAGCCATCCTTAAACGG 59.576 50.000 0.00 0.00 32.20 4.44
2291 3231 2.423538 CCCAGAAAGCCATCCTTAAACG 59.576 50.000 0.00 0.00 32.20 3.60
2300 3240 1.428912 TCCAACTTCCCAGAAAGCCAT 59.571 47.619 0.00 0.00 0.00 4.40
2307 3247 0.772124 AAGGCCTCCAACTTCCCAGA 60.772 55.000 5.23 0.00 0.00 3.86
2310 3250 1.304464 CCAAGGCCTCCAACTTCCC 60.304 63.158 5.23 0.00 0.00 3.97
2312 3252 0.693049 TCTCCAAGGCCTCCAACTTC 59.307 55.000 5.23 0.00 0.00 3.01
2323 3265 2.818714 CGCAGCAGCTCTCCAAGG 60.819 66.667 0.00 0.00 39.10 3.61
2331 3273 2.504163 CTTCTCTGACCGCAGCAGCT 62.504 60.000 0.00 0.00 42.01 4.24
2333 3275 1.447489 CCTTCTCTGACCGCAGCAG 60.447 63.158 0.00 0.00 42.01 4.24
2356 3298 0.474660 AGACCTCCACTCAAGCCCTT 60.475 55.000 0.00 0.00 0.00 3.95
2395 3337 2.904866 GGCTTCACCAACACGGCA 60.905 61.111 0.00 0.00 39.03 5.69
2400 3342 2.594303 CTGCCGGCTTCACCAACA 60.594 61.111 29.70 1.91 39.03 3.33
2422 3364 1.014044 CACCACACTGGATTCGTCCG 61.014 60.000 0.00 0.00 40.96 4.79
2433 3375 2.612972 CGCCATAGAAACTCACCACACT 60.613 50.000 0.00 0.00 0.00 3.55
2437 3379 0.392461 GCCGCCATAGAAACTCACCA 60.392 55.000 0.00 0.00 0.00 4.17
2465 3407 1.202582 CGTATTCTCCGATGGCCTAGG 59.797 57.143 3.67 3.67 0.00 3.02
2481 3423 3.069946 TTGTCGTCCCGGCCGTAT 61.070 61.111 26.12 0.00 0.00 3.06
2486 3428 3.853597 AACTCGTTGTCGTCCCGGC 62.854 63.158 0.00 0.00 38.33 6.13
2488 3430 2.078914 CGAACTCGTTGTCGTCCCG 61.079 63.158 0.00 0.00 38.33 5.14
2489 3431 0.109412 ATCGAACTCGTTGTCGTCCC 60.109 55.000 0.00 0.00 40.80 4.46
2490 3432 2.532531 TATCGAACTCGTTGTCGTCC 57.467 50.000 0.00 0.00 40.80 4.79
2492 3434 3.373130 TCTGATATCGAACTCGTTGTCGT 59.627 43.478 0.00 0.00 40.80 4.34
2493 3435 3.936661 TCTGATATCGAACTCGTTGTCG 58.063 45.455 0.00 0.00 40.80 4.35
2495 3437 5.096169 CAGTTCTGATATCGAACTCGTTGT 58.904 41.667 26.16 12.30 45.81 3.32
2496 3438 4.500837 CCAGTTCTGATATCGAACTCGTTG 59.499 45.833 26.16 19.66 45.81 4.10
2497 3439 4.398358 TCCAGTTCTGATATCGAACTCGTT 59.602 41.667 26.16 13.02 45.81 3.85
2509 3465 0.687354 ACGCCAAGTCCAGTTCTGAT 59.313 50.000 1.00 0.00 0.00 2.90
2515 3471 0.599204 CAACGTACGCCAAGTCCAGT 60.599 55.000 16.72 0.00 0.00 4.00
2519 3475 1.226030 AAGCCAACGTACGCCAAGTC 61.226 55.000 16.72 0.00 0.00 3.01
2531 3487 3.321968 AGAGACAAATTTCCCAAGCCAAC 59.678 43.478 0.00 0.00 0.00 3.77
2537 3493 3.069443 GCAACCAGAGACAAATTTCCCAA 59.931 43.478 0.00 0.00 0.00 4.12
2541 3497 4.590850 AAGGCAACCAGAGACAAATTTC 57.409 40.909 0.00 0.00 37.17 2.17
2553 3509 3.307480 GGAAGACTAGCTAAAGGCAACCA 60.307 47.826 0.00 0.00 44.79 3.67
2579 3535 1.210234 TCATGCCACCACTGATACCAG 59.790 52.381 0.00 0.00 45.76 4.00
2580 3536 1.284313 TCATGCCACCACTGATACCA 58.716 50.000 0.00 0.00 0.00 3.25
2581 3537 2.158769 TGATCATGCCACCACTGATACC 60.159 50.000 0.00 0.00 30.00 2.73
2582 3538 2.874701 GTGATCATGCCACCACTGATAC 59.125 50.000 0.00 0.00 30.00 2.24
2583 3539 2.773661 AGTGATCATGCCACCACTGATA 59.226 45.455 0.00 0.00 38.32 2.15
2584 3540 1.562942 AGTGATCATGCCACCACTGAT 59.437 47.619 0.00 0.00 38.32 2.90
2585 3541 0.986527 AGTGATCATGCCACCACTGA 59.013 50.000 0.00 0.00 38.32 3.41
2586 3542 1.741706 GAAGTGATCATGCCACCACTG 59.258 52.381 0.00 0.00 39.52 3.66
2587 3543 1.352017 TGAAGTGATCATGCCACCACT 59.648 47.619 0.00 8.29 41.14 4.00
2588 3544 1.825090 TGAAGTGATCATGCCACCAC 58.175 50.000 0.00 6.50 35.23 4.16
2589 3545 2.583024 TTGAAGTGATCATGCCACCA 57.417 45.000 0.00 4.48 38.03 4.17
2590 3546 4.178540 CAATTTGAAGTGATCATGCCACC 58.821 43.478 0.00 2.44 38.03 4.61
2591 3547 4.082081 TCCAATTTGAAGTGATCATGCCAC 60.082 41.667 0.00 9.23 38.03 5.01
2592 3548 4.087907 TCCAATTTGAAGTGATCATGCCA 58.912 39.130 0.00 0.00 38.03 4.92
2593 3549 4.441079 CCTCCAATTTGAAGTGATCATGCC 60.441 45.833 0.00 0.00 38.03 4.40
2594 3550 4.441079 CCCTCCAATTTGAAGTGATCATGC 60.441 45.833 0.00 0.00 38.03 4.06
2595 3551 4.951715 TCCCTCCAATTTGAAGTGATCATG 59.048 41.667 0.00 0.00 38.03 3.07
2596 3552 4.952335 GTCCCTCCAATTTGAAGTGATCAT 59.048 41.667 0.00 0.00 38.03 2.45
2597 3553 4.202556 TGTCCCTCCAATTTGAAGTGATCA 60.203 41.667 0.00 0.00 35.85 2.92
2598 3554 4.335416 TGTCCCTCCAATTTGAAGTGATC 58.665 43.478 0.00 0.00 0.00 2.92
2599 3555 4.387026 TGTCCCTCCAATTTGAAGTGAT 57.613 40.909 0.00 0.00 0.00 3.06
2600 3556 3.874383 TGTCCCTCCAATTTGAAGTGA 57.126 42.857 0.00 0.00 0.00 3.41
2601 3557 5.232463 CAATTGTCCCTCCAATTTGAAGTG 58.768 41.667 0.00 0.00 41.79 3.16
2602 3558 4.284234 CCAATTGTCCCTCCAATTTGAAGT 59.716 41.667 4.43 0.00 41.79 3.01
2603 3559 4.322953 CCCAATTGTCCCTCCAATTTGAAG 60.323 45.833 4.43 0.00 41.79 3.02
2604 3560 3.582208 CCCAATTGTCCCTCCAATTTGAA 59.418 43.478 4.43 0.00 41.79 2.69
2605 3561 3.172339 CCCAATTGTCCCTCCAATTTGA 58.828 45.455 4.43 0.00 41.79 2.69
2606 3562 2.355007 GCCCAATTGTCCCTCCAATTTG 60.355 50.000 4.43 0.00 41.79 2.32
2607 3563 1.908619 GCCCAATTGTCCCTCCAATTT 59.091 47.619 4.43 0.00 41.79 1.82
2608 3564 1.571955 GCCCAATTGTCCCTCCAATT 58.428 50.000 4.43 0.00 43.89 2.32
2609 3565 0.325577 GGCCCAATTGTCCCTCCAAT 60.326 55.000 4.43 0.00 36.62 3.16
2610 3566 1.078347 GGCCCAATTGTCCCTCCAA 59.922 57.895 4.43 0.00 0.00 3.53
2611 3567 1.734420 TTGGCCCAATTGTCCCTCCA 61.734 55.000 0.00 1.46 0.00 3.86
2612 3568 0.544120 TTTGGCCCAATTGTCCCTCC 60.544 55.000 0.00 0.00 0.00 4.30
2613 3569 1.571955 ATTTGGCCCAATTGTCCCTC 58.428 50.000 0.00 0.00 0.00 4.30
2614 3570 1.908619 GAATTTGGCCCAATTGTCCCT 59.091 47.619 18.94 0.00 0.00 4.20
2615 3571 1.065491 GGAATTTGGCCCAATTGTCCC 60.065 52.381 18.94 10.52 0.00 4.46
2616 3572 1.065491 GGGAATTTGGCCCAATTGTCC 60.065 52.381 18.94 14.30 45.31 4.02
2617 3573 2.401583 GGGAATTTGGCCCAATTGTC 57.598 50.000 18.94 10.67 45.31 3.18
2624 3580 2.159179 ACAGTATGGGAATTTGGCCC 57.841 50.000 0.00 0.00 43.62 5.80
2625 3581 5.669164 TTTTACAGTATGGGAATTTGGCC 57.331 39.130 0.00 0.00 43.62 5.36
2673 3629 7.603985 ACCCAGTGGAAAAGCAGATAGCTAC 62.604 48.000 11.95 0.00 44.37 3.58
2674 3630 5.612736 ACCCAGTGGAAAAGCAGATAGCTA 61.613 45.833 11.95 0.00 44.37 3.32
2675 3631 4.906550 ACCCAGTGGAAAAGCAGATAGCT 61.907 47.826 11.95 0.00 46.11 3.32
2676 3632 2.019984 CCCAGTGGAAAAGCAGATAGC 58.980 52.381 11.95 0.00 46.19 2.97
2677 3633 3.012518 CACCCAGTGGAAAAGCAGATAG 58.987 50.000 11.95 0.00 34.81 2.08
2678 3634 3.071874 CACCCAGTGGAAAAGCAGATA 57.928 47.619 11.95 0.00 34.81 1.98
2679 3635 1.915141 CACCCAGTGGAAAAGCAGAT 58.085 50.000 11.95 0.00 34.81 2.90
2680 3636 3.419793 CACCCAGTGGAAAAGCAGA 57.580 52.632 11.95 0.00 34.81 4.26
2690 3646 2.094675 CTTAAGCAATCCCACCCAGTG 58.905 52.381 0.00 0.00 0.00 3.66
2691 3647 1.616994 GCTTAAGCAATCCCACCCAGT 60.617 52.381 22.59 0.00 41.59 4.00
2692 3648 1.106285 GCTTAAGCAATCCCACCCAG 58.894 55.000 22.59 0.00 41.59 4.45
2693 3649 3.281332 GCTTAAGCAATCCCACCCA 57.719 52.632 22.59 0.00 41.59 4.51


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

AutoCloner maintained by Alex Coulton.