Multiple sequence alignment - TraesCS2D01G302600

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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 TraesCS2D01G302600 chr2D 100.000 3455 0 0 1 3455 386482608 386479154 0 6381
1 TraesCS2D01G302600 chr2D 95.616 593 25 1 1 592 562895014 562895606 0 950
2 TraesCS2D01G302600 chr2A 94.455 2759 94 18 580 3325 522489764 522487052 0 4193
3 TraesCS2D01G302600 chr2A 95.447 593 25 2 1 591 651133854 651133262 0 944
4 TraesCS2D01G302600 chr2B 92.090 2718 115 38 580 3269 457337652 457335007 0 3736
5 TraesCS2D01G302600 chr5D 96.271 590 21 1 1 589 431561392 431561981 0 966
6 TraesCS2D01G302600 chr5D 94.941 593 28 2 1 592 174803303 174802712 0 928
7 TraesCS2D01G302600 chr7D 95.819 598 21 4 1 596 565208017 565207422 0 963
8 TraesCS2D01G302600 chr7D 95.593 590 21 2 1 589 562194130 562194715 0 941
9 TraesCS2D01G302600 chr5A 95.784 593 23 2 1 591 580928384 580927792 0 955
10 TraesCS2D01G302600 chr1D 95.278 593 27 1 1 592 469096254 469095662 0 939
11 TraesCS2D01G302600 chr1D 95.118 594 27 2 1 592 433908299 433907706 0 935


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 TraesCS2D01G302600 chr2D 386479154 386482608 3454 True 6381 6381 100.000 1 3455 1 chr2D.!!$R1 3454
1 TraesCS2D01G302600 chr2D 562895014 562895606 592 False 950 950 95.616 1 592 1 chr2D.!!$F1 591
2 TraesCS2D01G302600 chr2A 522487052 522489764 2712 True 4193 4193 94.455 580 3325 1 chr2A.!!$R1 2745
3 TraesCS2D01G302600 chr2A 651133262 651133854 592 True 944 944 95.447 1 591 1 chr2A.!!$R2 590
4 TraesCS2D01G302600 chr2B 457335007 457337652 2645 True 3736 3736 92.090 580 3269 1 chr2B.!!$R1 2689
5 TraesCS2D01G302600 chr5D 431561392 431561981 589 False 966 966 96.271 1 589 1 chr5D.!!$F1 588
6 TraesCS2D01G302600 chr5D 174802712 174803303 591 True 928 928 94.941 1 592 1 chr5D.!!$R1 591
7 TraesCS2D01G302600 chr7D 565207422 565208017 595 True 963 963 95.819 1 596 1 chr7D.!!$R1 595
8 TraesCS2D01G302600 chr7D 562194130 562194715 585 False 941 941 95.593 1 589 1 chr7D.!!$F1 588
9 TraesCS2D01G302600 chr5A 580927792 580928384 592 True 955 955 95.784 1 591 1 chr5A.!!$R1 590
10 TraesCS2D01G302600 chr1D 469095662 469096254 592 True 939 939 95.278 1 592 1 chr1D.!!$R2 591
11 TraesCS2D01G302600 chr1D 433907706 433908299 593 True 935 935 95.118 1 592 1 chr1D.!!$R1 591

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
920 933 0.798776 CGCCCATCTCCATTAATCGC 59.201 55.0 0.00 0.0 0.0 4.58 F
1982 2007 0.599204 GACAAGGTCGACGAAGGCAA 60.599 55.0 9.92 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2131 0.179018 TCTCGATGGCGATCCTCTCA 60.179 55.0 2.84 0.0 46.8 3.27 R
3394 3442 0.036388 GCCGGTTTGAGACATCCAGA 60.036 55.0 1.90 0.0 0.0 3.86 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
233 237 2.118233 TTGTATGCCGGCAGGTGTGA 62.118 55.000 35.36 15.14 40.50 3.58
281 285 1.002087 GTGGTCGAACTCAAGTCCCAT 59.998 52.381 0.33 0.00 0.00 4.00
554 560 2.468831 GACAAAAAGCGGACAAATGCA 58.531 42.857 0.00 0.00 0.00 3.96
602 608 1.227118 GCTCTTAGCGGTGGAGCTC 60.227 63.158 25.93 4.71 45.67 4.09
920 933 0.798776 CGCCCATCTCCATTAATCGC 59.201 55.000 0.00 0.00 0.00 4.58
923 936 1.442769 CCATCTCCATTAATCGCCGG 58.557 55.000 0.00 0.00 0.00 6.13
924 937 1.001974 CCATCTCCATTAATCGCCGGA 59.998 52.381 5.05 0.00 0.00 5.14
925 938 2.549992 CCATCTCCATTAATCGCCGGAA 60.550 50.000 5.05 0.00 0.00 4.30
1188 1201 2.101770 GATCACGACGACGGGGAC 59.898 66.667 10.08 0.47 43.75 4.46
1593 1618 2.124983 CAGTGGCCGTCCCTGATG 60.125 66.667 0.00 0.00 34.52 3.07
1631 1656 1.835927 GCCACCACAAGCTCCTCTCT 61.836 60.000 0.00 0.00 0.00 3.10
1982 2007 0.599204 GACAAGGTCGACGAAGGCAA 60.599 55.000 9.92 0.00 0.00 4.52
2478 2503 0.381445 CGCGCCCATTCATTCATTCA 59.619 50.000 0.00 0.00 0.00 2.57
2532 2557 5.643777 TCATCCGATTCTTCTTGGTTTCTTC 59.356 40.000 0.00 0.00 0.00 2.87
2533 2558 5.228945 TCCGATTCTTCTTGGTTTCTTCT 57.771 39.130 0.00 0.00 0.00 2.85
2534 2559 5.621193 TCCGATTCTTCTTGGTTTCTTCTT 58.379 37.500 0.00 0.00 0.00 2.52
2552 2577 5.418840 TCTTCTTCATTGGTTCCTTATTGGC 59.581 40.000 0.00 0.00 35.26 4.52
2553 2578 4.671831 TCTTCATTGGTTCCTTATTGGCA 58.328 39.130 0.00 0.00 35.26 4.92
2554 2579 4.706476 TCTTCATTGGTTCCTTATTGGCAG 59.294 41.667 0.00 0.00 35.26 4.85
2555 2580 4.314522 TCATTGGTTCCTTATTGGCAGA 57.685 40.909 0.00 0.00 35.26 4.26
2737 2774 5.376854 AATTAACTGCATCACGAGCTTTT 57.623 34.783 0.00 0.00 0.00 2.27
2738 2775 2.693797 AACTGCATCACGAGCTTTTG 57.306 45.000 0.00 0.00 0.00 2.44
2753 2790 3.570559 GCTTTTGCGCACTAATTAACCA 58.429 40.909 11.12 0.00 34.86 3.67
2754 2791 4.173256 GCTTTTGCGCACTAATTAACCAT 58.827 39.130 11.12 0.00 34.86 3.55
2755 2792 4.625311 GCTTTTGCGCACTAATTAACCATT 59.375 37.500 11.12 0.00 34.86 3.16
2756 2793 5.444481 GCTTTTGCGCACTAATTAACCATTG 60.444 40.000 11.12 0.00 34.86 2.82
2757 2794 3.773860 TGCGCACTAATTAACCATTGG 57.226 42.857 5.66 0.00 0.00 3.16
2758 2795 3.085533 TGCGCACTAATTAACCATTGGT 58.914 40.909 5.66 1.37 37.05 3.67
2760 2797 4.021894 TGCGCACTAATTAACCATTGGTTT 60.022 37.500 25.34 11.05 44.33 3.27
2761 2798 4.926832 GCGCACTAATTAACCATTGGTTTT 59.073 37.500 25.34 16.73 44.33 2.43
2762 2799 5.407084 GCGCACTAATTAACCATTGGTTTTT 59.593 36.000 25.34 19.88 44.33 1.94
2803 2840 8.958119 TGGTTGGTAGTGATGAGATTTAATAC 57.042 34.615 0.00 0.00 0.00 1.89
2815 2852 6.693466 TGAGATTTAATACGGTGAGTTGACA 58.307 36.000 0.00 0.00 0.00 3.58
2822 2859 6.627395 AATACGGTGAGTTGACAAATCAAA 57.373 33.333 19.03 6.77 46.40 2.69
3094 3137 7.266966 CAGATAGCGTTGTTGAAATATAATGCG 59.733 37.037 0.00 0.00 39.39 4.73
3128 3171 0.242825 TCTTCCGGTACTCAAGCACG 59.757 55.000 0.00 0.00 0.00 5.34
3251 3299 3.150767 CCGGTGGTTTGACTTTCCAATA 58.849 45.455 0.00 0.00 32.82 1.90
3280 3328 1.105457 GCATGCTAGTGGCCATTTGA 58.895 50.000 9.72 0.00 40.92 2.69
3285 3333 2.225467 GCTAGTGGCCATTTGATCCTC 58.775 52.381 9.72 0.00 34.27 3.71
3288 3336 1.918262 AGTGGCCATTTGATCCTCTGA 59.082 47.619 9.72 0.00 0.00 3.27
3309 3357 3.996921 TCGTGAGAGGTAGTACTCCTT 57.003 47.619 13.14 0.00 38.26 3.36
3320 3368 7.473795 AGAGGTAGTACTCCTTAGAGCATCTAC 60.474 44.444 13.14 0.00 42.09 2.59
3328 3376 4.453093 GAGCATCTACAGCCTGCC 57.547 61.111 0.00 0.00 36.56 4.85
3329 3377 1.227793 GAGCATCTACAGCCTGCCC 60.228 63.158 0.00 0.00 36.56 5.36
3330 3378 2.203266 GCATCTACAGCCTGCCCC 60.203 66.667 0.00 0.00 0.00 5.80
3331 3379 2.512896 CATCTACAGCCTGCCCCC 59.487 66.667 0.00 0.00 0.00 5.40
3332 3380 2.074948 CATCTACAGCCTGCCCCCT 61.075 63.158 0.00 0.00 0.00 4.79
3333 3381 0.764369 CATCTACAGCCTGCCCCCTA 60.764 60.000 0.00 0.00 0.00 3.53
3334 3382 0.030092 ATCTACAGCCTGCCCCCTAA 60.030 55.000 0.00 0.00 0.00 2.69
3335 3383 0.252974 TCTACAGCCTGCCCCCTAAA 60.253 55.000 0.00 0.00 0.00 1.85
3336 3384 0.623723 CTACAGCCTGCCCCCTAAAA 59.376 55.000 0.00 0.00 0.00 1.52
3337 3385 0.330267 TACAGCCTGCCCCCTAAAAC 59.670 55.000 0.00 0.00 0.00 2.43
3338 3386 1.682344 CAGCCTGCCCCCTAAAACC 60.682 63.158 0.00 0.00 0.00 3.27
3339 3387 2.754254 GCCTGCCCCCTAAAACCG 60.754 66.667 0.00 0.00 0.00 4.44
3340 3388 2.761160 CCTGCCCCCTAAAACCGT 59.239 61.111 0.00 0.00 0.00 4.83
3341 3389 1.378119 CCTGCCCCCTAAAACCGTC 60.378 63.158 0.00 0.00 0.00 4.79
3342 3390 1.683441 CTGCCCCCTAAAACCGTCT 59.317 57.895 0.00 0.00 0.00 4.18
3343 3391 0.392595 CTGCCCCCTAAAACCGTCTC 60.393 60.000 0.00 0.00 0.00 3.36
3344 3392 1.128809 TGCCCCCTAAAACCGTCTCA 61.129 55.000 0.00 0.00 0.00 3.27
3345 3393 0.037160 GCCCCCTAAAACCGTCTCAA 59.963 55.000 0.00 0.00 0.00 3.02
3346 3394 1.546099 GCCCCCTAAAACCGTCTCAAA 60.546 52.381 0.00 0.00 0.00 2.69
3347 3395 2.882643 GCCCCCTAAAACCGTCTCAAAT 60.883 50.000 0.00 0.00 0.00 2.32
3348 3396 2.752903 CCCCCTAAAACCGTCTCAAATG 59.247 50.000 0.00 0.00 0.00 2.32
3349 3397 2.163613 CCCCTAAAACCGTCTCAAATGC 59.836 50.000 0.00 0.00 0.00 3.56
3350 3398 3.081804 CCCTAAAACCGTCTCAAATGCT 58.918 45.455 0.00 0.00 0.00 3.79
3351 3399 3.506067 CCCTAAAACCGTCTCAAATGCTT 59.494 43.478 0.00 0.00 0.00 3.91
3352 3400 4.698304 CCCTAAAACCGTCTCAAATGCTTA 59.302 41.667 0.00 0.00 0.00 3.09
3353 3401 5.182380 CCCTAAAACCGTCTCAAATGCTTAA 59.818 40.000 0.00 0.00 0.00 1.85
3354 3402 6.294286 CCCTAAAACCGTCTCAAATGCTTAAA 60.294 38.462 0.00 0.00 0.00 1.52
3355 3403 6.581166 CCTAAAACCGTCTCAAATGCTTAAAC 59.419 38.462 0.00 0.00 0.00 2.01
3356 3404 4.499037 AACCGTCTCAAATGCTTAAACC 57.501 40.909 0.00 0.00 0.00 3.27
3357 3405 3.482436 ACCGTCTCAAATGCTTAAACCA 58.518 40.909 0.00 0.00 0.00 3.67
3358 3406 3.502211 ACCGTCTCAAATGCTTAAACCAG 59.498 43.478 0.00 0.00 0.00 4.00
3359 3407 3.502211 CCGTCTCAAATGCTTAAACCAGT 59.498 43.478 0.00 0.00 0.00 4.00
3360 3408 4.378459 CCGTCTCAAATGCTTAAACCAGTC 60.378 45.833 0.00 0.00 0.00 3.51
3361 3409 4.452455 CGTCTCAAATGCTTAAACCAGTCT 59.548 41.667 0.00 0.00 0.00 3.24
3362 3410 5.049405 CGTCTCAAATGCTTAAACCAGTCTT 60.049 40.000 0.00 0.00 0.00 3.01
3363 3411 6.147164 CGTCTCAAATGCTTAAACCAGTCTTA 59.853 38.462 0.00 0.00 0.00 2.10
3364 3412 7.307751 CGTCTCAAATGCTTAAACCAGTCTTAA 60.308 37.037 0.00 0.00 0.00 1.85
3365 3413 8.349983 GTCTCAAATGCTTAAACCAGTCTTAAA 58.650 33.333 0.00 0.00 0.00 1.52
3366 3414 9.077885 TCTCAAATGCTTAAACCAGTCTTAAAT 57.922 29.630 0.00 0.00 0.00 1.40
3367 3415 9.132521 CTCAAATGCTTAAACCAGTCTTAAATG 57.867 33.333 0.00 0.00 0.00 2.32
3368 3416 7.598493 TCAAATGCTTAAACCAGTCTTAAATGC 59.402 33.333 0.00 0.00 0.00 3.56
3369 3417 6.840780 ATGCTTAAACCAGTCTTAAATGCT 57.159 33.333 0.00 0.00 0.00 3.79
3370 3418 6.254281 TGCTTAAACCAGTCTTAAATGCTC 57.746 37.500 0.00 0.00 0.00 4.26
3371 3419 5.767665 TGCTTAAACCAGTCTTAAATGCTCA 59.232 36.000 0.00 0.00 0.00 4.26
3372 3420 6.434028 TGCTTAAACCAGTCTTAAATGCTCAT 59.566 34.615 0.00 0.00 0.00 2.90
3373 3421 6.969473 GCTTAAACCAGTCTTAAATGCTCATC 59.031 38.462 0.00 0.00 0.00 2.92
3374 3422 5.551760 AAACCAGTCTTAAATGCTCATCG 57.448 39.130 0.00 0.00 0.00 3.84
3375 3423 3.535561 ACCAGTCTTAAATGCTCATCGG 58.464 45.455 0.00 0.00 0.00 4.18
3376 3424 3.055094 ACCAGTCTTAAATGCTCATCGGT 60.055 43.478 0.00 0.00 0.00 4.69
3377 3425 3.557595 CCAGTCTTAAATGCTCATCGGTC 59.442 47.826 0.00 0.00 0.00 4.79
3378 3426 4.183865 CAGTCTTAAATGCTCATCGGTCA 58.816 43.478 0.00 0.00 0.00 4.02
3379 3427 4.033358 CAGTCTTAAATGCTCATCGGTCAC 59.967 45.833 0.00 0.00 0.00 3.67
3380 3428 3.932710 GTCTTAAATGCTCATCGGTCACA 59.067 43.478 0.00 0.00 0.00 3.58
3381 3429 4.391830 GTCTTAAATGCTCATCGGTCACAA 59.608 41.667 0.00 0.00 0.00 3.33
3382 3430 5.000591 TCTTAAATGCTCATCGGTCACAAA 58.999 37.500 0.00 0.00 0.00 2.83
3383 3431 5.471797 TCTTAAATGCTCATCGGTCACAAAA 59.528 36.000 0.00 0.00 0.00 2.44
3384 3432 4.582701 AAATGCTCATCGGTCACAAAAA 57.417 36.364 0.00 0.00 0.00 1.94
3404 3452 5.350504 AAAATCGACTCATCTGGATGTCT 57.649 39.130 9.94 0.00 39.72 3.41
3405 3453 4.582701 AATCGACTCATCTGGATGTCTC 57.417 45.455 9.94 5.66 39.72 3.36
3406 3454 3.004752 TCGACTCATCTGGATGTCTCA 57.995 47.619 9.94 0.00 39.72 3.27
3407 3455 3.356290 TCGACTCATCTGGATGTCTCAA 58.644 45.455 9.94 0.00 39.72 3.02
3408 3456 3.763897 TCGACTCATCTGGATGTCTCAAA 59.236 43.478 9.94 0.00 39.72 2.69
3409 3457 3.862267 CGACTCATCTGGATGTCTCAAAC 59.138 47.826 9.94 0.00 39.72 2.93
3410 3458 4.187694 GACTCATCTGGATGTCTCAAACC 58.812 47.826 9.94 0.00 39.72 3.27
3411 3459 3.193263 CTCATCTGGATGTCTCAAACCG 58.807 50.000 9.94 0.00 39.72 4.44
3412 3460 2.093500 TCATCTGGATGTCTCAAACCGG 60.093 50.000 0.00 0.00 39.72 5.28
3413 3461 0.036388 TCTGGATGTCTCAAACCGGC 60.036 55.000 0.00 0.00 0.00 6.13
3414 3462 1.002624 TGGATGTCTCAAACCGGCC 60.003 57.895 0.00 0.00 0.00 6.13
3415 3463 1.299976 GGATGTCTCAAACCGGCCT 59.700 57.895 0.00 0.00 0.00 5.19
3416 3464 0.744771 GGATGTCTCAAACCGGCCTC 60.745 60.000 0.00 0.00 0.00 4.70
3417 3465 0.036388 GATGTCTCAAACCGGCCTCA 60.036 55.000 0.00 0.00 0.00 3.86
3418 3466 0.400213 ATGTCTCAAACCGGCCTCAA 59.600 50.000 0.00 0.00 0.00 3.02
3419 3467 0.181587 TGTCTCAAACCGGCCTCAAA 59.818 50.000 0.00 0.00 0.00 2.69
3420 3468 0.591659 GTCTCAAACCGGCCTCAAAC 59.408 55.000 0.00 0.00 0.00 2.93
3421 3469 0.882927 TCTCAAACCGGCCTCAAACG 60.883 55.000 0.00 0.00 0.00 3.60
3422 3470 1.153127 TCAAACCGGCCTCAAACGT 60.153 52.632 0.00 0.00 0.00 3.99
3423 3471 1.161563 TCAAACCGGCCTCAAACGTC 61.162 55.000 0.00 0.00 0.00 4.34
3424 3472 1.147600 AAACCGGCCTCAAACGTCT 59.852 52.632 0.00 0.00 0.00 4.18
3425 3473 1.164041 AAACCGGCCTCAAACGTCTG 61.164 55.000 0.00 0.00 0.00 3.51
3426 3474 2.742372 CCGGCCTCAAACGTCTGG 60.742 66.667 0.00 0.00 0.00 3.86
3427 3475 2.742372 CGGCCTCAAACGTCTGGG 60.742 66.667 0.00 0.00 0.00 4.45
3428 3476 3.056328 GGCCTCAAACGTCTGGGC 61.056 66.667 11.60 11.60 41.80 5.36
3429 3477 3.056328 GCCTCAAACGTCTGGGCC 61.056 66.667 9.49 0.00 37.12 5.80
3430 3478 2.429930 CCTCAAACGTCTGGGCCA 59.570 61.111 5.85 5.85 0.00 5.36
3431 3479 1.002134 CCTCAAACGTCTGGGCCAT 60.002 57.895 6.72 0.00 0.00 4.40
3432 3480 1.026718 CCTCAAACGTCTGGGCCATC 61.027 60.000 6.72 2.31 0.00 3.51
3433 3481 0.321564 CTCAAACGTCTGGGCCATCA 60.322 55.000 6.72 0.00 0.00 3.07
3434 3482 0.321564 TCAAACGTCTGGGCCATCAG 60.322 55.000 6.72 3.41 36.17 2.90
3435 3483 0.321564 CAAACGTCTGGGCCATCAGA 60.322 55.000 6.72 6.31 41.03 3.27
3439 3487 3.785859 TCTGGGCCATCAGACGCC 61.786 66.667 6.72 2.10 44.92 5.68
3440 3488 3.790437 CTGGGCCATCAGACGCCT 61.790 66.667 6.72 0.00 45.01 5.52
3441 3489 3.746949 CTGGGCCATCAGACGCCTC 62.747 68.421 6.72 2.31 45.01 4.70
3442 3490 3.474570 GGGCCATCAGACGCCTCT 61.475 66.667 4.39 0.00 45.01 3.69
3443 3491 2.107953 GGCCATCAGACGCCTCTC 59.892 66.667 0.00 0.00 42.21 3.20
3444 3492 2.725312 GGCCATCAGACGCCTCTCA 61.725 63.158 0.00 0.00 42.21 3.27
3445 3493 1.445095 GCCATCAGACGCCTCTCAT 59.555 57.895 0.00 0.00 0.00 2.90
3446 3494 0.676184 GCCATCAGACGCCTCTCATA 59.324 55.000 0.00 0.00 0.00 2.15
3447 3495 1.274728 GCCATCAGACGCCTCTCATAT 59.725 52.381 0.00 0.00 0.00 1.78
3448 3496 2.673610 GCCATCAGACGCCTCTCATATC 60.674 54.545 0.00 0.00 0.00 1.63
3449 3497 2.094286 CCATCAGACGCCTCTCATATCC 60.094 54.545 0.00 0.00 0.00 2.59
3450 3498 2.364972 TCAGACGCCTCTCATATCCA 57.635 50.000 0.00 0.00 0.00 3.41
3451 3499 2.234143 TCAGACGCCTCTCATATCCAG 58.766 52.381 0.00 0.00 0.00 3.86
3452 3500 0.965439 AGACGCCTCTCATATCCAGC 59.035 55.000 0.00 0.00 0.00 4.85
3453 3501 0.037790 GACGCCTCTCATATCCAGCC 60.038 60.000 0.00 0.00 0.00 4.85
3454 3502 1.294780 CGCCTCTCATATCCAGCCC 59.705 63.158 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.609072 GAGCCACTTCTTTCGCCTTTT 59.391 47.619 0.00 0.00 0.00 2.27
233 237 4.082523 CTCCCGTGGTCATGCCGT 62.083 66.667 0.00 0.00 41.21 5.68
327 331 5.181811 CAGAAAATACCACAGTTCATGCTGA 59.818 40.000 7.27 0.00 39.62 4.26
440 444 3.368220 CCCATTTCATGTCCGCATTCAAA 60.368 43.478 0.00 0.00 31.99 2.69
1113 1126 3.190849 CTCATGACAGTGGCGCGG 61.191 66.667 8.83 0.00 0.00 6.46
1282 1295 2.656069 GCCGGTAGACCTCCTGCAA 61.656 63.158 1.90 0.00 35.72 4.08
1335 1348 4.014065 GCGAAGTAGGATGCGACC 57.986 61.111 0.00 0.00 0.00 4.79
1341 1354 2.412112 GCGTCCGCGAAGTAGGAT 59.588 61.111 8.23 0.00 41.33 3.24
1404 1417 2.275081 CGAGTCGTCGTCGTCGTC 60.275 66.667 11.41 6.41 41.57 4.20
1593 1618 3.119096 GCGTCGGAAAGGGACTGC 61.119 66.667 0.00 0.00 40.86 4.40
1620 1645 1.862911 TGGGAGGATAGAGAGGAGCTT 59.137 52.381 0.00 0.00 0.00 3.74
1711 1736 4.379243 CTCCGTGTCCCGCAGCTT 62.379 66.667 0.00 0.00 34.38 3.74
1886 1911 0.693430 ATCCCATGAGCTCTGCCTCA 60.693 55.000 16.19 0.00 45.16 3.86
1892 1917 2.865598 CGCGGATCCCATGAGCTCT 61.866 63.158 16.19 0.00 0.00 4.09
1991 2016 1.373590 GCATCTTCCGGCGCCTTTAA 61.374 55.000 26.68 14.43 0.00 1.52
1992 2017 1.817941 GCATCTTCCGGCGCCTTTA 60.818 57.895 26.68 6.49 0.00 1.85
2106 2131 0.179018 TCTCGATGGCGATCCTCTCA 60.179 55.000 2.84 0.00 46.80 3.27
2206 2231 2.030562 CCAACCGCGACTCACCTT 59.969 61.111 8.23 0.00 0.00 3.50
2209 2234 2.027625 CCTTCCAACCGCGACTCAC 61.028 63.158 8.23 0.00 0.00 3.51
2429 2454 0.736325 CTCGTTCTTGCCGACCGATT 60.736 55.000 0.00 0.00 35.95 3.34
2478 2503 8.731605 CACGGTCTATCACAATATCTATGTACT 58.268 37.037 0.00 0.00 0.00 2.73
2491 2516 1.253100 TGAGCACACGGTCTATCACA 58.747 50.000 0.00 0.00 40.44 3.58
2532 2557 4.706476 TCTGCCAATAAGGAACCAATGAAG 59.294 41.667 0.00 0.00 41.22 3.02
2533 2558 4.671831 TCTGCCAATAAGGAACCAATGAA 58.328 39.130 0.00 0.00 41.22 2.57
2534 2559 4.018506 TCTCTGCCAATAAGGAACCAATGA 60.019 41.667 0.00 0.00 41.22 2.57
2552 2577 4.885907 AGAATCAAGCTCTCTCTCTCTCTG 59.114 45.833 0.00 0.00 0.00 3.35
2553 2578 5.121380 AGAATCAAGCTCTCTCTCTCTCT 57.879 43.478 0.00 0.00 0.00 3.10
2554 2579 5.841957 AAGAATCAAGCTCTCTCTCTCTC 57.158 43.478 0.00 0.00 0.00 3.20
2555 2580 6.426587 ACTAAGAATCAAGCTCTCTCTCTCT 58.573 40.000 0.00 0.00 0.00 3.10
2650 2681 9.769093 TGAACGTACGTATGAATATGATATCAG 57.231 33.333 23.12 0.00 0.00 2.90
2737 2774 3.085533 ACCAATGGTTAATTAGTGCGCA 58.914 40.909 5.66 5.66 27.29 6.09
2738 2775 3.775661 ACCAATGGTTAATTAGTGCGC 57.224 42.857 0.00 0.00 27.29 6.09
2803 2840 4.285807 TGTTTGATTTGTCAACTCACCG 57.714 40.909 5.18 0.00 0.00 4.94
2815 2852 7.706281 TGCACGATTTTGTTATGTTTGATTT 57.294 28.000 0.00 0.00 0.00 2.17
2822 2859 4.235939 TGCTTGCACGATTTTGTTATGT 57.764 36.364 0.00 0.00 0.00 2.29
3076 3119 5.275881 GCAGCACGCATTATATTTCAACAAC 60.276 40.000 0.00 0.00 41.79 3.32
3094 3137 1.336240 GGAAGACACAAATGGCAGCAC 60.336 52.381 0.00 0.00 35.60 4.40
3223 3271 3.301554 CAAACCACCGGCATGCCA 61.302 61.111 34.93 0.00 35.37 4.92
3251 3299 3.067742 GCCACTAGCATGCATGAAAGATT 59.932 43.478 30.64 8.23 42.97 2.40
3285 3333 3.810941 GGAGTACTACCTCTCACGATCAG 59.189 52.174 0.00 0.00 32.93 2.90
3288 3336 4.506937 AAGGAGTACTACCTCTCACGAT 57.493 45.455 0.00 0.00 36.67 3.73
3297 3345 6.297582 TGTAGATGCTCTAAGGAGTACTACC 58.702 44.000 0.00 2.33 41.38 3.18
3309 3357 1.043816 GGCAGGCTGTAGATGCTCTA 58.956 55.000 17.16 0.00 39.88 2.43
3320 3368 1.682344 GGTTTTAGGGGGCAGGCTG 60.682 63.158 10.94 10.94 0.00 4.85
3325 3373 1.128809 TGAGACGGTTTTAGGGGGCA 61.129 55.000 0.00 0.00 0.00 5.36
3326 3374 0.037160 TTGAGACGGTTTTAGGGGGC 59.963 55.000 0.00 0.00 0.00 5.80
3327 3375 2.572209 TTTGAGACGGTTTTAGGGGG 57.428 50.000 0.00 0.00 0.00 5.40
3328 3376 2.163613 GCATTTGAGACGGTTTTAGGGG 59.836 50.000 0.00 0.00 0.00 4.79
3329 3377 3.081804 AGCATTTGAGACGGTTTTAGGG 58.918 45.455 0.00 0.00 0.00 3.53
3330 3378 4.766404 AAGCATTTGAGACGGTTTTAGG 57.234 40.909 0.00 0.00 0.00 2.69
3331 3379 6.581166 GGTTTAAGCATTTGAGACGGTTTTAG 59.419 38.462 0.00 0.00 0.00 1.85
3332 3380 6.039493 TGGTTTAAGCATTTGAGACGGTTTTA 59.961 34.615 0.00 0.00 0.00 1.52
3333 3381 5.163499 TGGTTTAAGCATTTGAGACGGTTTT 60.163 36.000 0.00 0.00 0.00 2.43
3334 3382 4.339814 TGGTTTAAGCATTTGAGACGGTTT 59.660 37.500 0.00 0.00 0.00 3.27
3335 3383 3.886505 TGGTTTAAGCATTTGAGACGGTT 59.113 39.130 0.00 0.00 0.00 4.44
3336 3384 3.482436 TGGTTTAAGCATTTGAGACGGT 58.518 40.909 0.00 0.00 0.00 4.83
3337 3385 3.502211 ACTGGTTTAAGCATTTGAGACGG 59.498 43.478 0.00 0.00 0.00 4.79
3338 3386 4.452455 AGACTGGTTTAAGCATTTGAGACG 59.548 41.667 0.00 0.00 0.00 4.18
3339 3387 5.948992 AGACTGGTTTAAGCATTTGAGAC 57.051 39.130 0.00 0.00 0.00 3.36
3340 3388 8.458573 TTTAAGACTGGTTTAAGCATTTGAGA 57.541 30.769 0.00 0.00 0.00 3.27
3341 3389 9.132521 CATTTAAGACTGGTTTAAGCATTTGAG 57.867 33.333 0.00 0.00 0.00 3.02
3342 3390 7.598493 GCATTTAAGACTGGTTTAAGCATTTGA 59.402 33.333 0.00 0.00 0.00 2.69
3343 3391 7.599998 AGCATTTAAGACTGGTTTAAGCATTTG 59.400 33.333 0.00 0.00 0.00 2.32
3344 3392 7.670364 AGCATTTAAGACTGGTTTAAGCATTT 58.330 30.769 0.00 0.00 0.00 2.32
3345 3393 7.039784 TGAGCATTTAAGACTGGTTTAAGCATT 60.040 33.333 0.00 0.00 0.00 3.56
3346 3394 6.434028 TGAGCATTTAAGACTGGTTTAAGCAT 59.566 34.615 0.00 0.00 0.00 3.79
3347 3395 5.767665 TGAGCATTTAAGACTGGTTTAAGCA 59.232 36.000 0.00 0.00 0.00 3.91
3348 3396 6.254281 TGAGCATTTAAGACTGGTTTAAGC 57.746 37.500 0.00 0.00 0.00 3.09
3349 3397 7.182761 CGATGAGCATTTAAGACTGGTTTAAG 58.817 38.462 0.00 0.00 0.00 1.85
3350 3398 6.093495 CCGATGAGCATTTAAGACTGGTTTAA 59.907 38.462 0.00 0.00 0.00 1.52
3351 3399 5.584649 CCGATGAGCATTTAAGACTGGTTTA 59.415 40.000 0.00 0.00 0.00 2.01
3352 3400 4.396166 CCGATGAGCATTTAAGACTGGTTT 59.604 41.667 0.00 0.00 0.00 3.27
3353 3401 3.941483 CCGATGAGCATTTAAGACTGGTT 59.059 43.478 0.00 0.00 0.00 3.67
3354 3402 3.055094 ACCGATGAGCATTTAAGACTGGT 60.055 43.478 0.00 0.00 0.00 4.00
3355 3403 3.535561 ACCGATGAGCATTTAAGACTGG 58.464 45.455 0.00 0.00 0.00 4.00
3356 3404 4.033358 GTGACCGATGAGCATTTAAGACTG 59.967 45.833 0.00 0.00 0.00 3.51
3357 3405 4.184629 GTGACCGATGAGCATTTAAGACT 58.815 43.478 0.00 0.00 0.00 3.24
3358 3406 3.932710 TGTGACCGATGAGCATTTAAGAC 59.067 43.478 0.00 0.00 0.00 3.01
3359 3407 4.200838 TGTGACCGATGAGCATTTAAGA 57.799 40.909 0.00 0.00 0.00 2.10
3360 3408 4.944962 TTGTGACCGATGAGCATTTAAG 57.055 40.909 0.00 0.00 0.00 1.85
3361 3409 5.697473 TTTTGTGACCGATGAGCATTTAA 57.303 34.783 0.00 0.00 0.00 1.52
3362 3410 5.697473 TTTTTGTGACCGATGAGCATTTA 57.303 34.783 0.00 0.00 0.00 1.40
3363 3411 4.582701 TTTTTGTGACCGATGAGCATTT 57.417 36.364 0.00 0.00 0.00 2.32
3381 3429 5.738909 AGACATCCAGATGAGTCGATTTTT 58.261 37.500 14.42 0.00 41.20 1.94
3382 3430 5.105187 TGAGACATCCAGATGAGTCGATTTT 60.105 40.000 14.42 0.00 41.20 1.82
3383 3431 4.403752 TGAGACATCCAGATGAGTCGATTT 59.596 41.667 14.42 0.00 41.20 2.17
3384 3432 3.956848 TGAGACATCCAGATGAGTCGATT 59.043 43.478 14.42 0.00 41.20 3.34
3385 3433 3.560105 TGAGACATCCAGATGAGTCGAT 58.440 45.455 14.42 0.00 41.20 3.59
3386 3434 3.004752 TGAGACATCCAGATGAGTCGA 57.995 47.619 14.42 0.00 41.20 4.20
3387 3435 3.790152 TTGAGACATCCAGATGAGTCG 57.210 47.619 14.42 0.00 41.20 4.18
3388 3436 4.187694 GGTTTGAGACATCCAGATGAGTC 58.812 47.826 14.42 10.00 41.20 3.36
3389 3437 3.368843 CGGTTTGAGACATCCAGATGAGT 60.369 47.826 14.42 0.85 41.20 3.41
3390 3438 3.193263 CGGTTTGAGACATCCAGATGAG 58.807 50.000 14.42 0.00 41.20 2.90
3391 3439 2.093500 CCGGTTTGAGACATCCAGATGA 60.093 50.000 14.42 0.00 41.20 2.92
3392 3440 2.283298 CCGGTTTGAGACATCCAGATG 58.717 52.381 6.09 6.09 44.15 2.90
3393 3441 1.407437 GCCGGTTTGAGACATCCAGAT 60.407 52.381 1.90 0.00 0.00 2.90
3394 3442 0.036388 GCCGGTTTGAGACATCCAGA 60.036 55.000 1.90 0.00 0.00 3.86
3395 3443 1.026718 GGCCGGTTTGAGACATCCAG 61.027 60.000 1.90 0.00 0.00 3.86
3396 3444 1.002624 GGCCGGTTTGAGACATCCA 60.003 57.895 1.90 0.00 0.00 3.41
3397 3445 0.744771 GAGGCCGGTTTGAGACATCC 60.745 60.000 1.90 0.00 0.00 3.51
3398 3446 0.036388 TGAGGCCGGTTTGAGACATC 60.036 55.000 1.90 0.00 0.00 3.06
3399 3447 0.400213 TTGAGGCCGGTTTGAGACAT 59.600 50.000 1.90 0.00 0.00 3.06
3400 3448 0.181587 TTTGAGGCCGGTTTGAGACA 59.818 50.000 1.90 0.00 0.00 3.41
3401 3449 0.591659 GTTTGAGGCCGGTTTGAGAC 59.408 55.000 1.90 0.00 0.00 3.36
3402 3450 0.882927 CGTTTGAGGCCGGTTTGAGA 60.883 55.000 1.90 0.00 0.00 3.27
3403 3451 1.164041 ACGTTTGAGGCCGGTTTGAG 61.164 55.000 1.90 0.00 0.00 3.02
3404 3452 1.153127 ACGTTTGAGGCCGGTTTGA 60.153 52.632 1.90 0.00 0.00 2.69
3405 3453 1.164041 AGACGTTTGAGGCCGGTTTG 61.164 55.000 1.90 0.00 0.00 2.93
3406 3454 1.147600 AGACGTTTGAGGCCGGTTT 59.852 52.632 1.90 0.00 0.00 3.27
3407 3455 1.597027 CAGACGTTTGAGGCCGGTT 60.597 57.895 1.90 0.00 0.00 4.44
3408 3456 2.030562 CAGACGTTTGAGGCCGGT 59.969 61.111 1.90 0.00 0.00 5.28
3409 3457 2.742372 CCAGACGTTTGAGGCCGG 60.742 66.667 7.81 0.00 0.00 6.13
3410 3458 2.742372 CCCAGACGTTTGAGGCCG 60.742 66.667 7.81 0.00 0.00 6.13
3411 3459 3.056328 GCCCAGACGTTTGAGGCC 61.056 66.667 20.75 0.00 37.66 5.19
3412 3460 3.056328 GGCCCAGACGTTTGAGGC 61.056 66.667 22.29 22.29 43.09 4.70
3413 3461 1.002134 ATGGCCCAGACGTTTGAGG 60.002 57.895 7.81 8.30 0.00 3.86
3414 3462 0.321564 TGATGGCCCAGACGTTTGAG 60.322 55.000 7.81 0.00 0.00 3.02
3415 3463 0.321564 CTGATGGCCCAGACGTTTGA 60.322 55.000 7.81 0.00 36.29 2.69
3416 3464 0.321564 TCTGATGGCCCAGACGTTTG 60.322 55.000 7.56 0.00 38.18 2.93
3417 3465 2.066340 TCTGATGGCCCAGACGTTT 58.934 52.632 7.56 0.00 38.18 3.60
3418 3466 3.805928 TCTGATGGCCCAGACGTT 58.194 55.556 7.56 0.00 38.18 3.99
3422 3470 3.785859 GGCGTCTGATGGCCCAGA 61.786 66.667 12.06 7.56 43.64 3.86
3427 3475 0.676184 TATGAGAGGCGTCTGATGGC 59.324 55.000 14.78 14.98 30.97 4.40
3428 3476 2.094286 GGATATGAGAGGCGTCTGATGG 60.094 54.545 14.78 0.00 30.97 3.51
3429 3477 2.560105 TGGATATGAGAGGCGTCTGATG 59.440 50.000 14.78 0.00 30.97 3.07
3430 3478 2.824936 CTGGATATGAGAGGCGTCTGAT 59.175 50.000 14.78 13.73 30.97 2.90
3431 3479 2.234143 CTGGATATGAGAGGCGTCTGA 58.766 52.381 14.78 5.70 30.97 3.27
3432 3480 1.336702 GCTGGATATGAGAGGCGTCTG 60.337 57.143 14.78 0.00 30.97 3.51
3433 3481 0.965439 GCTGGATATGAGAGGCGTCT 59.035 55.000 9.04 9.04 34.86 4.18
3434 3482 0.037790 GGCTGGATATGAGAGGCGTC 60.038 60.000 0.00 0.00 0.00 5.19
3435 3483 1.476007 GGGCTGGATATGAGAGGCGT 61.476 60.000 0.00 0.00 33.18 5.68
3436 3484 1.294780 GGGCTGGATATGAGAGGCG 59.705 63.158 0.00 0.00 33.18 5.52


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

AutoCloner maintained by Alex Coulton.