Multiple sequence alignment - TraesCS5A01G217300

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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 TraesCS5A01G217300 chr5A 100.000 3548 0 0 1 3548 434133944 434137491 0.000000e+00 6553
1 TraesCS5A01G217300 chr5D 90.930 3550 177 47 1 3505 333052468 333055917 0.000000e+00 4638
2 TraesCS5A01G217300 chr5D 74.012 658 141 25 1568 2208 503049168 503049812 1.270000e-59 241
3 TraesCS5A01G217300 chr5B 90.000 3560 187 72 5 3505 389155481 389158930 0.000000e+00 4446
4 TraesCS5A01G217300 chr5B 74.127 630 141 21 1568 2184 631826630 631827250 1.270000e-59 241
5 TraesCS5A01G217300 chr6B 91.756 279 18 3 3271 3548 52078069 52078343 2.000000e-102 383
6 TraesCS5A01G217300 chr6A 78.846 208 39 5 1709 1914 613664291 613664087 6.180000e-28 135


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 TraesCS5A01G217300 chr5A 434133944 434137491 3547 False 6553 6553 100.000 1 3548 1 chr5A.!!$F1 3547
1 TraesCS5A01G217300 chr5D 333052468 333055917 3449 False 4638 4638 90.930 1 3505 1 chr5D.!!$F1 3504
2 TraesCS5A01G217300 chr5D 503049168 503049812 644 False 241 241 74.012 1568 2208 1 chr5D.!!$F2 640
3 TraesCS5A01G217300 chr5B 389155481 389158930 3449 False 4446 4446 90.000 5 3505 1 chr5B.!!$F1 3500
4 TraesCS5A01G217300 chr5B 631826630 631827250 620 False 241 241 74.127 1568 2184 1 chr5B.!!$F2 616

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
655 679 0.178929 ATATCCCCCTCTCGGTCCAC 60.179 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2647 2713 1.523758 CGTTCTCCAGTGAAAAGGGG 58.476 55.0 0.0 0.0 0.0 4.79 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
24 25 6.081356 ACCCCTTGAACCATGAAGAAAATAA 58.919 36.000 0.00 0.00 0.00 1.40
132 133 4.817464 AGTAGAGGACAACTGCGTATAGAG 59.183 45.833 0.00 0.00 0.00 2.43
143 144 6.807708 ACTGCGTATAGAGTCGTTAAATTG 57.192 37.500 0.00 0.00 0.00 2.32
190 200 3.875727 CACATGGGTCATTCTGATCACTC 59.124 47.826 0.00 0.00 0.00 3.51
192 202 4.964897 ACATGGGTCATTCTGATCACTCTA 59.035 41.667 0.00 0.00 0.00 2.43
198 210 7.510343 TGGGTCATTCTGATCACTCTATCATTA 59.490 37.037 0.00 0.00 35.40 1.90
221 233 5.079689 TGTGTTATTCGATGGTTGAGCTA 57.920 39.130 0.00 0.00 0.00 3.32
232 244 1.604604 GTTGAGCTACCAAACAGCCA 58.395 50.000 0.00 0.00 39.99 4.75
241 253 3.629142 ACCAAACAGCCATAGACCTAC 57.371 47.619 0.00 0.00 0.00 3.18
294 306 6.869421 AGTGAAAAATTCAGTTTTCGTGTG 57.131 33.333 7.70 0.00 46.16 3.82
295 307 6.616947 AGTGAAAAATTCAGTTTTCGTGTGA 58.383 32.000 7.70 0.00 46.16 3.58
301 313 3.254470 TCAGTTTTCGTGTGAGTTCCA 57.746 42.857 0.00 0.00 0.00 3.53
311 323 1.666700 TGTGAGTTCCACCGAAAAACG 59.333 47.619 0.00 0.00 45.09 3.60
344 356 3.760537 TGTTTCCGTTTCCGTGAAAAAG 58.239 40.909 1.37 0.46 36.07 2.27
345 357 3.439476 TGTTTCCGTTTCCGTGAAAAAGA 59.561 39.130 1.37 0.11 36.07 2.52
346 358 4.082895 TGTTTCCGTTTCCGTGAAAAAGAA 60.083 37.500 1.37 5.07 36.07 2.52
348 360 4.904253 TCCGTTTCCGTGAAAAAGAATT 57.096 36.364 1.37 0.00 33.14 2.17
350 362 3.978855 CCGTTTCCGTGAAAAAGAATTCC 59.021 43.478 0.65 0.00 33.14 3.01
351 363 3.662186 CGTTTCCGTGAAAAAGAATTCCG 59.338 43.478 0.65 0.00 33.14 4.30
352 364 2.981400 TCCGTGAAAAAGAATTCCGC 57.019 45.000 0.65 0.00 0.00 5.54
354 366 2.882137 TCCGTGAAAAAGAATTCCGCTT 59.118 40.909 0.65 0.00 0.00 4.68
355 367 3.058501 TCCGTGAAAAAGAATTCCGCTTC 60.059 43.478 0.65 3.23 0.00 3.86
356 368 3.058224 CCGTGAAAAAGAATTCCGCTTCT 60.058 43.478 0.65 0.00 37.06 2.85
357 369 4.153475 CCGTGAAAAAGAATTCCGCTTCTA 59.847 41.667 0.65 0.00 34.40 2.10
358 370 5.080068 CGTGAAAAAGAATTCCGCTTCTAC 58.920 41.667 0.65 3.65 34.40 2.59
359 371 5.107065 CGTGAAAAAGAATTCCGCTTCTACT 60.107 40.000 0.65 0.00 34.40 2.57
376 388 7.010738 CGCTTCTACTTTTCCGTTTCCATATTA 59.989 37.037 0.00 0.00 0.00 0.98
391 403 8.388853 GTTTCCATATTACCTCTTCGTTTTCTC 58.611 37.037 0.00 0.00 0.00 2.87
392 404 6.579865 TCCATATTACCTCTTCGTTTTCTCC 58.420 40.000 0.00 0.00 0.00 3.71
398 410 5.037383 ACCTCTTCGTTTTCTCCTTTTCT 57.963 39.130 0.00 0.00 0.00 2.52
402 414 2.762745 TCGTTTTCTCCTTTTCTCCGG 58.237 47.619 0.00 0.00 0.00 5.14
464 480 3.064271 CAGACTTTTCGTTCCGTTTTCCA 59.936 43.478 0.00 0.00 0.00 3.53
489 511 2.031437 CCGAAAAACACGGTTCCGTTTA 59.969 45.455 14.42 0.00 44.57 2.01
492 514 5.390779 CCGAAAAACACGGTTCCGTTTATAT 60.391 40.000 14.42 1.68 44.57 0.86
493 515 5.505446 CGAAAAACACGGTTCCGTTTATATG 59.495 40.000 14.42 5.08 40.97 1.78
494 516 5.945466 AAAACACGGTTCCGTTTATATGT 57.055 34.783 14.42 5.70 40.97 2.29
495 517 7.432350 AAAAACACGGTTCCGTTTATATGTA 57.568 32.000 14.42 0.00 40.97 2.29
496 518 7.432350 AAAACACGGTTCCGTTTATATGTAA 57.568 32.000 14.42 0.00 40.97 2.41
537 559 4.469469 TCTGTTTTCCAATTTCCTCCCT 57.531 40.909 0.00 0.00 0.00 4.20
550 572 7.318893 CAATTTCCTCCCTGATTCTCTTTTTC 58.681 38.462 0.00 0.00 0.00 2.29
601 623 6.287525 TCATTTTCATCCTTGTTTTCAACCC 58.712 36.000 0.00 0.00 35.77 4.11
655 679 0.178929 ATATCCCCCTCTCGGTCCAC 60.179 60.000 0.00 0.00 0.00 4.02
847 890 2.068821 TCCCCAGCTCATCTCAGCC 61.069 63.158 0.00 0.00 40.65 4.85
902 948 2.616842 TCGAAGGAAAACTTGTCCAAGC 59.383 45.455 6.94 0.00 41.99 4.01
957 1016 1.154654 CGCGTGCGTTTCTTCTTCC 60.155 57.895 6.00 0.00 34.35 3.46
977 1036 4.722700 CAAGTCCAGGCCGGGTGG 62.723 72.222 22.25 12.72 36.28 4.61
1980 2046 4.508128 GGCGCGATCGACCAGGAA 62.508 66.667 21.57 0.00 37.90 3.36
2209 2275 5.010933 TCAAGAACTACCTCTGTCTCGAAT 58.989 41.667 0.00 0.00 0.00 3.34
2210 2276 5.124138 TCAAGAACTACCTCTGTCTCGAATC 59.876 44.000 0.00 0.00 0.00 2.52
2212 2278 2.290464 ACTACCTCTGTCTCGAATCCG 58.710 52.381 0.00 0.00 37.07 4.18
2213 2279 1.604755 CTACCTCTGTCTCGAATCCGG 59.395 57.143 0.00 0.00 36.24 5.14
2214 2280 1.066587 CCTCTGTCTCGAATCCGGC 59.933 63.158 0.00 0.00 36.24 6.13
2354 2420 4.173924 GGAGGAGCTGCTGGAGGC 62.174 72.222 14.48 0.00 42.22 4.70
2398 2464 4.719369 GTCTCGACGGCGGCAAGT 62.719 66.667 15.54 0.00 38.28 3.16
2505 2571 3.426568 GGCAAGGACAGCTGCGAC 61.427 66.667 15.27 4.00 39.55 5.19
2645 2711 5.578727 GGTCACGCCATATTCAGATATTCTC 59.421 44.000 0.00 0.00 37.17 2.87
2647 2713 4.872691 CACGCCATATTCAGATATTCTCCC 59.127 45.833 0.00 0.00 0.00 4.30
2670 2738 2.554032 CCTTTTCACTGGAGAACGCAAT 59.446 45.455 0.00 0.00 0.00 3.56
2691 2759 4.019919 TGCGATGCAAGAGAAAAATAGC 57.980 40.909 0.00 0.00 34.76 2.97
2747 2827 3.390175 AGTAGTGGCACTCCTAGATGT 57.610 47.619 25.80 0.00 0.00 3.06
2761 2841 7.920151 CACTCCTAGATGTATTCTCTTGAGTTG 59.080 40.741 0.00 0.00 35.86 3.16
2774 2854 7.321745 TCTCTTGAGTTGGTTTTCTTTTCTC 57.678 36.000 0.00 0.00 0.00 2.87
2775 2855 7.112779 TCTCTTGAGTTGGTTTTCTTTTCTCT 58.887 34.615 0.00 0.00 0.00 3.10
2776 2856 8.265055 TCTCTTGAGTTGGTTTTCTTTTCTCTA 58.735 33.333 0.00 0.00 0.00 2.43
2777 2857 8.980481 TCTTGAGTTGGTTTTCTTTTCTCTAT 57.020 30.769 0.00 0.00 0.00 1.98
2778 2858 9.057089 TCTTGAGTTGGTTTTCTTTTCTCTATC 57.943 33.333 0.00 0.00 0.00 2.08
2779 2859 7.745620 TGAGTTGGTTTTCTTTTCTCTATCC 57.254 36.000 0.00 0.00 0.00 2.59
2780 2860 7.518188 TGAGTTGGTTTTCTTTTCTCTATCCT 58.482 34.615 0.00 0.00 0.00 3.24
2781 2861 7.661847 TGAGTTGGTTTTCTTTTCTCTATCCTC 59.338 37.037 0.00 0.00 0.00 3.71
2782 2862 7.750655 AGTTGGTTTTCTTTTCTCTATCCTCT 58.249 34.615 0.00 0.00 0.00 3.69
2783 2863 8.881262 AGTTGGTTTTCTTTTCTCTATCCTCTA 58.119 33.333 0.00 0.00 0.00 2.43
2826 2906 1.953559 TTGAAGACTCACACTGGTGC 58.046 50.000 0.17 0.00 44.87 5.01
2828 2908 0.394565 GAAGACTCACACTGGTGCCT 59.605 55.000 0.17 0.00 44.87 4.75
3018 3106 3.267031 AGTTTATGGCCTCTTACCAAGCT 59.733 43.478 3.32 0.00 41.49 3.74
3040 3128 1.588404 GGATATGTGCACGTTCGTCTG 59.412 52.381 18.34 0.00 0.00 3.51
3041 3129 2.259618 GATATGTGCACGTTCGTCTGT 58.740 47.619 18.34 0.00 0.00 3.41
3042 3130 1.414378 TATGTGCACGTTCGTCTGTG 58.586 50.000 18.34 0.47 39.10 3.66
3043 3131 1.221466 ATGTGCACGTTCGTCTGTGG 61.221 55.000 13.13 0.00 36.61 4.17
3044 3132 2.964925 TGCACGTTCGTCTGTGGC 60.965 61.111 0.00 0.00 36.61 5.01
3045 3133 4.059459 GCACGTTCGTCTGTGGCG 62.059 66.667 0.00 0.00 36.61 5.69
3046 3134 4.059459 CACGTTCGTCTGTGGCGC 62.059 66.667 0.00 0.00 32.47 6.53
3047 3135 4.578898 ACGTTCGTCTGTGGCGCA 62.579 61.111 10.83 0.00 0.00 6.09
3048 3136 3.112075 CGTTCGTCTGTGGCGCAT 61.112 61.111 10.83 0.00 0.00 4.73
3049 3137 2.667318 CGTTCGTCTGTGGCGCATT 61.667 57.895 10.83 0.00 0.00 3.56
3050 3138 1.154413 GTTCGTCTGTGGCGCATTG 60.154 57.895 10.83 0.00 0.00 2.82
3051 3139 2.324330 TTCGTCTGTGGCGCATTGG 61.324 57.895 10.83 0.00 0.00 3.16
3052 3140 3.049674 CGTCTGTGGCGCATTGGT 61.050 61.111 10.83 0.00 0.00 3.67
3053 3141 2.616330 CGTCTGTGGCGCATTGGTT 61.616 57.895 10.83 0.00 0.00 3.67
3054 3142 1.659794 GTCTGTGGCGCATTGGTTT 59.340 52.632 10.83 0.00 0.00 3.27
3055 3143 0.878416 GTCTGTGGCGCATTGGTTTA 59.122 50.000 10.83 0.00 0.00 2.01
3056 3144 1.472480 GTCTGTGGCGCATTGGTTTAT 59.528 47.619 10.83 0.00 0.00 1.40
3057 3145 1.472082 TCTGTGGCGCATTGGTTTATG 59.528 47.619 10.83 0.00 0.00 1.90
3170 3258 0.034186 TTGGATCATGGGTCTGCACC 60.034 55.000 0.00 0.00 42.90 5.01
3211 3300 2.286121 CCCTACCCCTGGCCTTCA 60.286 66.667 3.32 0.00 0.00 3.02
3223 3312 3.826157 CCTGGCCTTCAATTTTCTACACA 59.174 43.478 3.32 0.00 0.00 3.72
3224 3313 4.082571 CCTGGCCTTCAATTTTCTACACAG 60.083 45.833 3.32 0.00 0.00 3.66
3253 3342 6.364435 ACGGACTAGAAAACGACTGTATTTTC 59.636 38.462 16.35 16.35 42.58 2.29
3304 3414 1.267383 GCCGTCGTGCACTTAATAAGC 60.267 52.381 16.19 4.87 0.00 3.09
3323 3433 7.907214 ATAAGCGTTGATCTTTTCTTGTACT 57.093 32.000 0.00 0.00 0.00 2.73
3324 3434 8.997621 ATAAGCGTTGATCTTTTCTTGTACTA 57.002 30.769 0.00 0.00 0.00 1.82
3325 3435 6.707599 AGCGTTGATCTTTTCTTGTACTAC 57.292 37.500 0.00 0.00 0.00 2.73
3326 3436 6.456501 AGCGTTGATCTTTTCTTGTACTACT 58.543 36.000 0.00 0.00 0.00 2.57
3327 3437 7.600065 AGCGTTGATCTTTTCTTGTACTACTA 58.400 34.615 0.00 0.00 0.00 1.82
3328 3438 7.541437 AGCGTTGATCTTTTCTTGTACTACTAC 59.459 37.037 0.00 0.00 0.00 2.73
3329 3439 7.541437 GCGTTGATCTTTTCTTGTACTACTACT 59.459 37.037 0.00 0.00 0.00 2.57
3330 3440 9.063739 CGTTGATCTTTTCTTGTACTACTACTC 57.936 37.037 0.00 0.00 0.00 2.59
3331 3441 9.356433 GTTGATCTTTTCTTGTACTACTACTCC 57.644 37.037 0.00 0.00 0.00 3.85
3332 3442 8.645814 TGATCTTTTCTTGTACTACTACTCCA 57.354 34.615 0.00 0.00 0.00 3.86
3333 3443 9.085645 TGATCTTTTCTTGTACTACTACTCCAA 57.914 33.333 0.00 0.00 0.00 3.53
3346 3456 8.438676 ACTACTACTCCAATACAAATCAATGC 57.561 34.615 0.00 0.00 0.00 3.56
3348 3458 7.325660 ACTACTCCAATACAAATCAATGCAG 57.674 36.000 0.00 0.00 0.00 4.41
3353 3463 6.092092 TCCAATACAAATCAATGCAGAAACG 58.908 36.000 0.00 0.00 0.00 3.60
3354 3464 5.289193 CCAATACAAATCAATGCAGAAACGG 59.711 40.000 0.00 0.00 0.00 4.44
3355 3465 2.676076 ACAAATCAATGCAGAAACGGC 58.324 42.857 0.00 0.00 0.00 5.68
3356 3466 2.035704 ACAAATCAATGCAGAAACGGCA 59.964 40.909 0.00 0.00 46.66 5.69
3358 3468 3.598019 AATCAATGCAGAAACGGCAAT 57.402 38.095 0.00 0.00 45.60 3.56
3364 3474 3.383620 TGCAGAAACGGCAATTTGATT 57.616 38.095 0.00 0.00 38.54 2.57
3382 3492 2.505557 GCAATGAGCAGGCAACGC 60.506 61.111 0.00 0.00 44.79 4.84
3383 3493 2.202388 CAATGAGCAGGCAACGCG 60.202 61.111 3.53 3.53 46.39 6.01
3384 3494 2.358615 AATGAGCAGGCAACGCGA 60.359 55.556 15.93 0.00 46.39 5.87
3385 3495 2.680913 AATGAGCAGGCAACGCGAC 61.681 57.895 15.93 0.60 46.39 5.19
3400 3510 1.518572 CGACCCGGGTCTTCGAATG 60.519 63.158 42.65 26.14 42.54 2.67
3401 3511 1.153429 GACCCGGGTCTTCGAATGG 60.153 63.158 40.89 5.32 41.57 3.16
3409 3519 3.006967 CGGGTCTTCGAATGGGAATCTAT 59.993 47.826 0.00 0.00 0.00 1.98
3420 3530 5.848286 ATGGGAATCTATGCATGTTCCTA 57.152 39.130 26.08 23.38 39.96 2.94
3436 3546 0.872021 CCTAGCGTGACATTCTCCGC 60.872 60.000 0.00 0.00 46.07 5.54
3442 3552 2.033662 GCGTGACATTCTCCGCTATTTC 60.034 50.000 0.58 0.00 42.66 2.17
3443 3553 2.540101 CGTGACATTCTCCGCTATTTCC 59.460 50.000 0.00 0.00 0.00 3.13
3446 3556 1.143073 ACATTCTCCGCTATTTCCCCC 59.857 52.381 0.00 0.00 0.00 5.40
3470 3580 1.998315 CTCGCTGGACATTCTCTGTTG 59.002 52.381 0.00 0.00 38.54 3.33
3475 3585 4.498009 CGCTGGACATTCTCTGTTGTTTTT 60.498 41.667 0.00 0.00 38.54 1.94
3476 3586 4.978580 GCTGGACATTCTCTGTTGTTTTTC 59.021 41.667 0.00 0.00 38.54 2.29
3477 3587 5.514274 TGGACATTCTCTGTTGTTTTTCC 57.486 39.130 0.00 0.00 38.54 3.13
3495 3605 2.379972 TCCTTCTCTCACTCGATTCCC 58.620 52.381 0.00 0.00 0.00 3.97
3496 3606 2.103373 CCTTCTCTCACTCGATTCCCA 58.897 52.381 0.00 0.00 0.00 4.37
3497 3607 2.697751 CCTTCTCTCACTCGATTCCCAT 59.302 50.000 0.00 0.00 0.00 4.00
3498 3608 3.492309 CCTTCTCTCACTCGATTCCCATG 60.492 52.174 0.00 0.00 0.00 3.66
3499 3609 2.739943 TCTCTCACTCGATTCCCATGT 58.260 47.619 0.00 0.00 0.00 3.21
3500 3610 2.428530 TCTCTCACTCGATTCCCATGTG 59.571 50.000 0.00 0.00 0.00 3.21
3502 3612 0.107703 TCACTCGATTCCCATGTGCC 60.108 55.000 0.00 0.00 0.00 5.01
3503 3613 0.107508 CACTCGATTCCCATGTGCCT 60.108 55.000 0.00 0.00 0.00 4.75
3504 3614 0.107508 ACTCGATTCCCATGTGCCTG 60.108 55.000 0.00 0.00 0.00 4.85
3505 3615 0.107508 CTCGATTCCCATGTGCCTGT 60.108 55.000 0.00 0.00 0.00 4.00
3506 3616 0.327924 TCGATTCCCATGTGCCTGTT 59.672 50.000 0.00 0.00 0.00 3.16
3507 3617 1.176527 CGATTCCCATGTGCCTGTTT 58.823 50.000 0.00 0.00 0.00 2.83
3508 3618 1.135315 CGATTCCCATGTGCCTGTTTG 60.135 52.381 0.00 0.00 0.00 2.93
3509 3619 1.205417 GATTCCCATGTGCCTGTTTGG 59.795 52.381 0.00 0.00 39.35 3.28
3510 3620 0.187117 TTCCCATGTGCCTGTTTGGA 59.813 50.000 0.00 0.00 38.35 3.53
3511 3621 0.251297 TCCCATGTGCCTGTTTGGAG 60.251 55.000 0.00 0.00 38.35 3.86
3512 3622 1.588082 CCATGTGCCTGTTTGGAGC 59.412 57.895 0.00 0.00 38.35 4.70
3513 3623 1.210931 CATGTGCCTGTTTGGAGCG 59.789 57.895 0.00 0.00 38.35 5.03
3514 3624 2.629656 ATGTGCCTGTTTGGAGCGC 61.630 57.895 0.00 0.00 38.35 5.92
3515 3625 2.980233 GTGCCTGTTTGGAGCGCT 60.980 61.111 11.27 11.27 38.35 5.92
3516 3626 2.979676 TGCCTGTTTGGAGCGCTG 60.980 61.111 18.48 0.00 38.35 5.18
3517 3627 4.410743 GCCTGTTTGGAGCGCTGC 62.411 66.667 23.36 23.36 38.35 5.25
3518 3628 3.741476 CCTGTTTGGAGCGCTGCC 61.741 66.667 26.87 20.82 38.35 4.85
3519 3629 2.670934 CTGTTTGGAGCGCTGCCT 60.671 61.111 26.87 0.00 0.00 4.75
3520 3630 2.974489 CTGTTTGGAGCGCTGCCTG 61.974 63.158 26.87 10.99 0.00 4.85
3521 3631 4.410743 GTTTGGAGCGCTGCCTGC 62.411 66.667 26.87 11.91 38.57 4.85
3522 3632 4.953010 TTTGGAGCGCTGCCTGCA 62.953 61.111 26.87 5.32 43.06 4.41
3523 3633 4.953010 TTGGAGCGCTGCCTGCAA 62.953 61.111 26.87 11.93 40.23 4.08
3524 3634 4.953010 TGGAGCGCTGCCTGCAAA 62.953 61.111 26.87 2.94 43.06 3.68
3525 3635 3.673484 GGAGCGCTGCCTGCAAAA 61.673 61.111 18.48 0.00 43.06 2.44
3526 3636 2.570181 GAGCGCTGCCTGCAAAAT 59.430 55.556 18.48 0.00 43.06 1.82
3527 3637 1.515736 GAGCGCTGCCTGCAAAATC 60.516 57.895 18.48 0.00 43.06 2.17
3528 3638 2.203972 GAGCGCTGCCTGCAAAATCA 62.204 55.000 18.48 0.00 43.06 2.57
3529 3639 1.373246 GCGCTGCCTGCAAAATCAA 60.373 52.632 0.00 0.00 43.06 2.57
3530 3640 0.945265 GCGCTGCCTGCAAAATCAAA 60.945 50.000 0.00 0.00 43.06 2.69
3531 3641 1.065358 CGCTGCCTGCAAAATCAAAG 58.935 50.000 0.00 0.00 43.06 2.77
3532 3642 1.435577 GCTGCCTGCAAAATCAAAGG 58.564 50.000 0.00 0.00 42.31 3.11
3533 3643 1.001181 GCTGCCTGCAAAATCAAAGGA 59.999 47.619 0.00 0.00 42.31 3.36
3534 3644 2.354403 GCTGCCTGCAAAATCAAAGGAT 60.354 45.455 0.00 0.00 42.31 3.24
3535 3645 3.119029 GCTGCCTGCAAAATCAAAGGATA 60.119 43.478 0.00 0.00 42.31 2.59
3536 3646 4.442472 GCTGCCTGCAAAATCAAAGGATAT 60.442 41.667 0.00 0.00 42.31 1.63
3537 3647 5.221303 GCTGCCTGCAAAATCAAAGGATATA 60.221 40.000 0.00 0.00 42.31 0.86
3538 3648 6.517864 GCTGCCTGCAAAATCAAAGGATATAT 60.518 38.462 0.00 0.00 42.31 0.86
3539 3649 6.985117 TGCCTGCAAAATCAAAGGATATATC 58.015 36.000 3.96 3.96 32.09 1.63
3540 3650 6.550481 TGCCTGCAAAATCAAAGGATATATCA 59.450 34.615 14.60 0.00 32.09 2.15
3541 3651 7.233962 TGCCTGCAAAATCAAAGGATATATCAT 59.766 33.333 14.60 4.42 32.09 2.45
3542 3652 7.544566 GCCTGCAAAATCAAAGGATATATCATG 59.455 37.037 14.60 9.85 32.09 3.07
3543 3653 8.799367 CCTGCAAAATCAAAGGATATATCATGA 58.201 33.333 14.60 14.22 32.09 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 9.503427 GTAGCCATGTTAACAATTGATTAAGTC 57.497 33.333 13.23 3.99 0.00 3.01
99 100 6.407074 GCAGTTGTCCTCTACTACCACAATAT 60.407 42.308 0.00 0.00 34.77 1.28
113 114 3.546417 CGACTCTATACGCAGTTGTCCTC 60.546 52.174 0.00 0.00 37.78 3.71
132 133 1.069500 AGCACGCACCAATTTAACGAC 60.069 47.619 0.00 0.00 0.00 4.34
143 144 2.365408 AACTTCTACTAGCACGCACC 57.635 50.000 0.00 0.00 0.00 5.01
192 202 8.675705 TCAACCATCGAATAACACATAATGAT 57.324 30.769 0.00 0.00 0.00 2.45
198 210 4.517285 AGCTCAACCATCGAATAACACAT 58.483 39.130 0.00 0.00 0.00 3.21
221 233 2.910319 TGTAGGTCTATGGCTGTTTGGT 59.090 45.455 0.00 0.00 0.00 3.67
250 262 8.827832 TCACTTTCATGAATATGGAATTTCCT 57.172 30.769 16.25 5.06 37.46 3.36
267 279 7.596995 ACACGAAAACTGAATTTTTCACTTTCA 59.403 29.630 8.58 0.00 43.06 2.69
272 284 6.526674 ACTCACACGAAAACTGAATTTTTCAC 59.473 34.615 8.58 0.00 43.06 3.18
273 285 6.616947 ACTCACACGAAAACTGAATTTTTCA 58.383 32.000 8.58 0.00 43.06 2.69
279 291 4.035208 GTGGAACTCACACGAAAACTGAAT 59.965 41.667 0.00 0.00 45.39 2.57
294 306 0.383860 CGCGTTTTTCGGTGGAACTC 60.384 55.000 0.00 0.00 40.26 3.01
295 307 1.644913 CGCGTTTTTCGGTGGAACT 59.355 52.632 0.00 0.00 40.26 3.01
311 323 0.723459 CGGAAACAAAACGTAGCCGC 60.723 55.000 0.00 0.00 37.54 6.53
344 356 3.683340 ACGGAAAAGTAGAAGCGGAATTC 59.317 43.478 0.00 0.00 0.00 2.17
345 357 3.671716 ACGGAAAAGTAGAAGCGGAATT 58.328 40.909 0.00 0.00 0.00 2.17
346 358 3.329929 ACGGAAAAGTAGAAGCGGAAT 57.670 42.857 0.00 0.00 0.00 3.01
348 360 2.825861 AACGGAAAAGTAGAAGCGGA 57.174 45.000 0.00 0.00 0.00 5.54
350 362 2.803956 TGGAAACGGAAAAGTAGAAGCG 59.196 45.455 0.00 0.00 0.00 4.68
351 363 6.679327 ATATGGAAACGGAAAAGTAGAAGC 57.321 37.500 0.00 0.00 0.00 3.86
352 364 8.610035 GGTAATATGGAAACGGAAAAGTAGAAG 58.390 37.037 0.00 0.00 0.00 2.85
354 366 7.854337 AGGTAATATGGAAACGGAAAAGTAGA 58.146 34.615 0.00 0.00 0.00 2.59
355 367 7.985752 AGAGGTAATATGGAAACGGAAAAGTAG 59.014 37.037 0.00 0.00 0.00 2.57
356 368 7.854337 AGAGGTAATATGGAAACGGAAAAGTA 58.146 34.615 0.00 0.00 0.00 2.24
357 369 6.718294 AGAGGTAATATGGAAACGGAAAAGT 58.282 36.000 0.00 0.00 0.00 2.66
358 370 7.465513 CGAAGAGGTAATATGGAAACGGAAAAG 60.466 40.741 0.00 0.00 0.00 2.27
359 371 6.314400 CGAAGAGGTAATATGGAAACGGAAAA 59.686 38.462 0.00 0.00 0.00 2.29
376 388 5.037383 AGAAAAGGAGAAAACGAAGAGGT 57.963 39.130 0.00 0.00 0.00 3.85
398 410 1.600485 GAAACGTTCTGCTTTTCCGGA 59.400 47.619 0.00 0.00 31.51 5.14
550 572 6.672118 GCAAAAACTTTTCACTTTTTCGGAGG 60.672 38.462 0.00 0.00 29.08 4.30
562 584 8.397148 GGATGAAAATGAAGCAAAAACTTTTCA 58.603 29.630 9.78 9.78 42.99 2.69
564 586 8.510243 AGGATGAAAATGAAGCAAAAACTTTT 57.490 26.923 0.00 0.00 0.00 2.27
601 623 3.610911 GATCCTGTTGGGTTTGGTAGAG 58.389 50.000 0.00 0.00 36.25 2.43
655 679 5.984323 CACATACCATGAGAGATCTTCACTG 59.016 44.000 0.00 4.23 0.00 3.66
847 890 3.006003 GCGAGGGTTTTATAGGAGGAGAG 59.994 52.174 0.00 0.00 0.00 3.20
884 928 2.039418 GGGCTTGGACAAGTTTTCCTT 58.961 47.619 13.08 0.00 40.45 3.36
902 948 2.281208 TGAAACGGCGAGGTTGGG 60.281 61.111 16.62 0.00 0.00 4.12
944 1003 2.480802 GACTTGGAGGAAGAAGAAACGC 59.519 50.000 0.00 0.00 35.42 4.84
945 1004 3.067833 GGACTTGGAGGAAGAAGAAACG 58.932 50.000 0.00 0.00 35.42 3.60
946 1005 4.068599 CTGGACTTGGAGGAAGAAGAAAC 58.931 47.826 0.00 0.00 35.42 2.78
947 1006 3.073062 CCTGGACTTGGAGGAAGAAGAAA 59.927 47.826 0.00 0.00 35.42 2.52
948 1007 2.639839 CCTGGACTTGGAGGAAGAAGAA 59.360 50.000 0.00 0.00 35.42 2.52
949 1008 2.260822 CCTGGACTTGGAGGAAGAAGA 58.739 52.381 0.00 0.00 35.42 2.87
950 1009 1.339535 GCCTGGACTTGGAGGAAGAAG 60.340 57.143 0.00 0.00 35.42 2.85
957 1016 4.101448 CCCGGCCTGGACTTGGAG 62.101 72.222 7.60 0.00 42.00 3.86
991 1050 1.012086 TACTCCTTCATCGTCGGTCG 58.988 55.000 0.00 0.00 41.41 4.79
999 1058 3.797184 GCATCGTCCAGTACTCCTTCATC 60.797 52.174 0.00 0.00 0.00 2.92
1581 1640 2.840753 GGGGTGCTTGAAGGGGACA 61.841 63.158 0.00 0.00 0.00 4.02
1746 1805 1.769098 CGATCATGCTGGACTTGCCG 61.769 60.000 0.00 0.00 40.66 5.69
2380 2446 4.717629 CTTGCCGCCGTCGAGACA 62.718 66.667 4.02 0.00 38.10 3.41
2382 2448 4.415332 GACTTGCCGCCGTCGAGA 62.415 66.667 0.00 0.00 38.10 4.04
2504 2570 3.054503 CCTCGTCCTGTCCGTCGT 61.055 66.667 0.00 0.00 0.00 4.34
2505 2571 2.745100 TCCTCGTCCTGTCCGTCG 60.745 66.667 0.00 0.00 0.00 5.12
2647 2713 1.523758 CGTTCTCCAGTGAAAAGGGG 58.476 55.000 0.00 0.00 0.00 4.79
2670 2738 3.181497 GGCTATTTTTCTCTTGCATCGCA 60.181 43.478 0.00 0.00 36.47 5.10
2681 2749 4.944317 CGGAAGAGGAAAGGCTATTTTTCT 59.056 41.667 0.00 0.00 35.42 2.52
2691 2759 4.119442 TCGAATAACGGAAGAGGAAAGG 57.881 45.455 0.00 0.00 42.82 3.11
2747 2827 9.408648 AGAAAAGAAAACCAACTCAAGAGAATA 57.591 29.630 3.73 0.00 0.00 1.75
2776 2856 9.362151 CTCTTTCTTCTTACCATAGTAGAGGAT 57.638 37.037 0.00 0.00 0.00 3.24
2777 2857 8.558312 TCTCTTTCTTCTTACCATAGTAGAGGA 58.442 37.037 0.00 0.00 0.00 3.71
2778 2858 8.754991 TCTCTTTCTTCTTACCATAGTAGAGG 57.245 38.462 0.00 0.00 0.00 3.69
2780 2860 9.702253 ACATCTCTTTCTTCTTACCATAGTAGA 57.298 33.333 0.00 0.00 0.00 2.59
2783 2863 9.442047 CAAACATCTCTTTCTTCTTACCATAGT 57.558 33.333 0.00 0.00 0.00 2.12
2826 2906 2.431260 GCACATGCCACGCAAAGG 60.431 61.111 0.00 0.00 43.62 3.11
2828 2908 1.591059 GTTGCACATGCCACGCAAA 60.591 52.632 12.31 0.00 46.37 3.68
3018 3106 1.996898 GACGAACGTGCACATATCCAA 59.003 47.619 18.64 0.00 0.00 3.53
3040 3128 2.094752 AGAACATAAACCAATGCGCCAC 60.095 45.455 4.18 0.00 0.00 5.01
3041 3129 2.166829 AGAACATAAACCAATGCGCCA 58.833 42.857 4.18 0.00 0.00 5.69
3042 3130 2.939460 AGAACATAAACCAATGCGCC 57.061 45.000 4.18 0.00 0.00 6.53
3043 3131 3.367630 CCAAAGAACATAAACCAATGCGC 59.632 43.478 0.00 0.00 0.00 6.09
3044 3132 4.804108 TCCAAAGAACATAAACCAATGCG 58.196 39.130 0.00 0.00 0.00 4.73
3045 3133 5.812127 GGATCCAAAGAACATAAACCAATGC 59.188 40.000 6.95 0.00 0.00 3.56
3046 3134 6.340522 GGGATCCAAAGAACATAAACCAATG 58.659 40.000 15.23 0.00 0.00 2.82
3047 3135 5.425217 GGGGATCCAAAGAACATAAACCAAT 59.575 40.000 15.23 0.00 0.00 3.16
3048 3136 4.775253 GGGGATCCAAAGAACATAAACCAA 59.225 41.667 15.23 0.00 0.00 3.67
3049 3137 4.045334 AGGGGATCCAAAGAACATAAACCA 59.955 41.667 15.23 0.00 34.83 3.67
3050 3138 4.402474 CAGGGGATCCAAAGAACATAAACC 59.598 45.833 15.23 0.04 34.83 3.27
3051 3139 5.016831 ACAGGGGATCCAAAGAACATAAAC 58.983 41.667 15.23 0.00 34.83 2.01
3052 3140 5.016173 CACAGGGGATCCAAAGAACATAAA 58.984 41.667 15.23 0.00 34.83 1.40
3053 3141 4.569653 CCACAGGGGATCCAAAGAACATAA 60.570 45.833 15.23 0.00 40.01 1.90
3054 3142 3.053693 CCACAGGGGATCCAAAGAACATA 60.054 47.826 15.23 0.00 40.01 2.29
3055 3143 2.291800 CCACAGGGGATCCAAAGAACAT 60.292 50.000 15.23 0.00 40.01 2.71
3056 3144 1.075374 CCACAGGGGATCCAAAGAACA 59.925 52.381 15.23 0.00 40.01 3.18
3057 3145 1.839424 CCACAGGGGATCCAAAGAAC 58.161 55.000 15.23 0.00 40.01 3.01
3114 3202 4.495828 GCATTATTTTTCTCCGAAAGCGTC 59.504 41.667 0.00 0.00 35.23 5.19
3170 3258 1.094073 GCTCATACAGTGCCTGCAGG 61.094 60.000 29.34 29.34 34.37 4.85
3211 3300 4.283722 AGTCCGTCCTCTGTGTAGAAAATT 59.716 41.667 0.00 0.00 31.21 1.82
3223 3312 2.487372 GTCGTTTTCTAGTCCGTCCTCT 59.513 50.000 0.00 0.00 0.00 3.69
3224 3313 2.487372 AGTCGTTTTCTAGTCCGTCCTC 59.513 50.000 0.00 0.00 0.00 3.71
3267 3356 7.589954 GCACGACGGCAGATAATAAAAATAAAT 59.410 33.333 0.00 0.00 0.00 1.40
3270 3359 5.524281 TGCACGACGGCAGATAATAAAAATA 59.476 36.000 6.88 0.00 39.25 1.40
3271 3360 4.334203 TGCACGACGGCAGATAATAAAAAT 59.666 37.500 6.88 0.00 39.25 1.82
3272 3361 3.685272 TGCACGACGGCAGATAATAAAAA 59.315 39.130 6.88 0.00 39.25 1.94
3273 3362 3.062909 GTGCACGACGGCAGATAATAAAA 59.937 43.478 0.00 0.00 45.96 1.52
3274 3363 2.605818 GTGCACGACGGCAGATAATAAA 59.394 45.455 0.00 0.00 45.96 1.40
3276 3365 1.407618 AGTGCACGACGGCAGATAATA 59.592 47.619 12.01 0.00 45.96 0.98
3277 3366 0.175760 AGTGCACGACGGCAGATAAT 59.824 50.000 12.01 0.00 45.96 1.28
3278 3367 0.037697 AAGTGCACGACGGCAGATAA 60.038 50.000 12.01 0.00 45.96 1.75
3279 3368 0.812549 TAAGTGCACGACGGCAGATA 59.187 50.000 12.01 5.46 45.96 1.98
3304 3414 8.967552 AGTAGTAGTACAAGAAAAGATCAACG 57.032 34.615 10.33 0.00 0.00 4.10
3322 3432 8.437360 TGCATTGATTTGTATTGGAGTAGTAG 57.563 34.615 0.00 0.00 0.00 2.57
3323 3433 8.264347 TCTGCATTGATTTGTATTGGAGTAGTA 58.736 33.333 0.00 0.00 0.00 1.82
3324 3434 7.112122 TCTGCATTGATTTGTATTGGAGTAGT 58.888 34.615 0.00 0.00 0.00 2.73
3325 3435 7.558161 TCTGCATTGATTTGTATTGGAGTAG 57.442 36.000 0.00 0.00 0.00 2.57
3326 3436 7.936496 TTCTGCATTGATTTGTATTGGAGTA 57.064 32.000 0.00 0.00 0.00 2.59
3327 3437 6.839124 TTCTGCATTGATTTGTATTGGAGT 57.161 33.333 0.00 0.00 0.00 3.85
3328 3438 6.252015 CGTTTCTGCATTGATTTGTATTGGAG 59.748 38.462 0.00 0.00 0.00 3.86
3329 3439 6.092092 CGTTTCTGCATTGATTTGTATTGGA 58.908 36.000 0.00 0.00 0.00 3.53
3330 3440 5.289193 CCGTTTCTGCATTGATTTGTATTGG 59.711 40.000 0.00 0.00 0.00 3.16
3331 3441 5.220265 GCCGTTTCTGCATTGATTTGTATTG 60.220 40.000 0.00 0.00 0.00 1.90
3332 3442 4.864247 GCCGTTTCTGCATTGATTTGTATT 59.136 37.500 0.00 0.00 0.00 1.89
3333 3443 4.082300 TGCCGTTTCTGCATTGATTTGTAT 60.082 37.500 0.00 0.00 32.85 2.29
3334 3444 3.254411 TGCCGTTTCTGCATTGATTTGTA 59.746 39.130 0.00 0.00 32.85 2.41
3335 3445 2.035704 TGCCGTTTCTGCATTGATTTGT 59.964 40.909 0.00 0.00 32.85 2.83
3336 3446 2.674954 TGCCGTTTCTGCATTGATTTG 58.325 42.857 0.00 0.00 32.85 2.32
3337 3447 3.383620 TTGCCGTTTCTGCATTGATTT 57.616 38.095 0.00 0.00 38.76 2.17
3338 3448 3.598019 ATTGCCGTTTCTGCATTGATT 57.402 38.095 0.00 0.00 38.76 2.57
3339 3449 3.598019 AATTGCCGTTTCTGCATTGAT 57.402 38.095 0.00 0.00 38.76 2.57
3340 3450 3.058450 CAAATTGCCGTTTCTGCATTGA 58.942 40.909 0.00 0.00 38.76 2.57
3341 3451 3.058450 TCAAATTGCCGTTTCTGCATTG 58.942 40.909 0.00 0.00 38.76 2.82
3342 3452 3.383620 TCAAATTGCCGTTTCTGCATT 57.616 38.095 0.00 0.00 38.76 3.56
3343 3453 3.598019 ATCAAATTGCCGTTTCTGCAT 57.402 38.095 0.00 0.00 38.76 3.96
3344 3454 3.058450 CAATCAAATTGCCGTTTCTGCA 58.942 40.909 0.00 0.00 36.84 4.41
3345 3455 3.710437 CAATCAAATTGCCGTTTCTGC 57.290 42.857 0.00 0.00 32.92 4.26
3367 3477 2.358615 TCGCGTTGCCTGCTCATT 60.359 55.556 5.77 0.00 0.00 2.57
3383 3493 1.153429 CCATTCGAAGACCCGGGTC 60.153 63.158 41.42 41.42 44.86 4.46
3384 3494 2.666098 CCCATTCGAAGACCCGGGT 61.666 63.158 30.81 30.81 35.45 5.28
3385 3495 1.906105 TTCCCATTCGAAGACCCGGG 61.906 60.000 22.25 22.25 39.95 5.73
3386 3496 0.180406 ATTCCCATTCGAAGACCCGG 59.820 55.000 3.35 0.00 34.32 5.73
3388 3498 4.319177 CATAGATTCCCATTCGAAGACCC 58.681 47.826 3.35 0.00 34.32 4.46
3389 3499 3.748568 GCATAGATTCCCATTCGAAGACC 59.251 47.826 3.35 0.00 34.32 3.85
3400 3510 4.006319 GCTAGGAACATGCATAGATTCCC 58.994 47.826 23.36 11.55 41.39 3.97
3401 3511 3.681897 CGCTAGGAACATGCATAGATTCC 59.318 47.826 21.08 21.08 40.87 3.01
3409 3519 0.320050 TGTCACGCTAGGAACATGCA 59.680 50.000 0.00 0.00 0.00 3.96
3446 3556 0.103937 GAGAATGTCCAGCGAGAGGG 59.896 60.000 0.00 0.00 0.00 4.30
3447 3557 1.110442 AGAGAATGTCCAGCGAGAGG 58.890 55.000 0.00 0.00 0.00 3.69
3452 3562 1.800805 ACAACAGAGAATGTCCAGCG 58.199 50.000 0.00 0.00 43.00 5.18
3456 3566 5.774498 AGGAAAAACAACAGAGAATGTCC 57.226 39.130 0.00 0.00 43.00 4.02
3470 3580 5.120986 GGAATCGAGTGAGAGAAGGAAAAAC 59.879 44.000 0.00 0.00 0.00 2.43
3475 3585 2.291605 TGGGAATCGAGTGAGAGAAGGA 60.292 50.000 0.00 0.00 0.00 3.36
3476 3586 2.103373 TGGGAATCGAGTGAGAGAAGG 58.897 52.381 0.00 0.00 0.00 3.46
3477 3587 3.131933 ACATGGGAATCGAGTGAGAGAAG 59.868 47.826 0.00 0.00 0.00 2.85
3495 3605 1.210931 CGCTCCAAACAGGCACATG 59.789 57.895 0.00 0.00 37.29 3.21
3496 3606 2.629656 GCGCTCCAAACAGGCACAT 61.630 57.895 0.00 0.00 37.29 3.21
3497 3607 3.286751 GCGCTCCAAACAGGCACA 61.287 61.111 0.00 0.00 37.29 4.57
3498 3608 2.980233 AGCGCTCCAAACAGGCAC 60.980 61.111 2.64 0.00 37.29 5.01
3499 3609 2.979676 CAGCGCTCCAAACAGGCA 60.980 61.111 7.13 0.00 37.29 4.75
3500 3610 4.410743 GCAGCGCTCCAAACAGGC 62.411 66.667 7.13 0.41 37.29 4.85
3502 3612 2.670934 AGGCAGCGCTCCAAACAG 60.671 61.111 22.44 6.49 0.00 3.16
3503 3613 2.979676 CAGGCAGCGCTCCAAACA 60.980 61.111 22.44 0.00 0.00 2.83
3504 3614 4.410743 GCAGGCAGCGCTCCAAAC 62.411 66.667 22.44 11.02 0.00 2.93
3512 3622 6.457132 TATCCTTTGATTTTGCAGGCAGCG 62.457 45.833 0.00 0.00 38.07 5.18
3513 3623 1.001181 TCCTTTGATTTTGCAGGCAGC 59.999 47.619 0.00 0.00 45.96 5.25
3514 3624 3.604875 ATCCTTTGATTTTGCAGGCAG 57.395 42.857 0.00 0.00 0.00 4.85
3515 3625 6.550481 TGATATATCCTTTGATTTTGCAGGCA 59.450 34.615 10.25 0.00 32.18 4.75
3516 3626 6.985117 TGATATATCCTTTGATTTTGCAGGC 58.015 36.000 10.25 0.00 32.18 4.85
3517 3627 8.799367 TCATGATATATCCTTTGATTTTGCAGG 58.201 33.333 10.25 0.00 32.18 4.85


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

AutoCloner maintained by Alex Coulton.