Multiple sequence alignment - TraesCS7D01G071500

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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 TraesCS7D01G071500 chr7D 100.000 3647 0 0 1 3647 42084820 42081174 0.000000e+00 6735.0
1 TraesCS7D01G071500 chr7D 93.364 3240 188 19 1 3224 42212203 42215431 0.000000e+00 4767.0
2 TraesCS7D01G071500 chr7D 92.825 3094 190 22 1 3079 41917430 41914354 0.000000e+00 4455.0
3 TraesCS7D01G071500 chr7D 87.097 155 18 2 3493 3647 42426496 42426648 1.350000e-39 174.0
4 TraesCS7D01G071500 chr7B 92.840 3240 201 21 1 3227 2564600 2561379 0.000000e+00 4669.0
5 TraesCS7D01G071500 chr4A 92.570 3230 205 24 1 3218 657366548 657369754 0.000000e+00 4602.0
6 TraesCS7D01G071500 chr4A 92.498 3239 202 22 1 3218 649144380 649147598 0.000000e+00 4597.0
7 TraesCS7D01G071500 chr4A 92.479 3231 210 21 1 3218 657306853 657310063 0.000000e+00 4590.0
8 TraesCS7D01G071500 chr4A 92.456 2757 171 21 471 3199 649184120 649186867 0.000000e+00 3904.0
9 TraesCS7D01G071500 chr4A 90.963 2722 194 23 532 3224 649056789 649059487 0.000000e+00 3616.0
10 TraesCS7D01G071500 chr4A 92.164 2093 137 15 1 2083 649173854 649175929 0.000000e+00 2931.0
11 TraesCS7D01G071500 chr4A 88.387 155 17 1 3493 3647 649116835 649116988 6.220000e-43 185.0
12 TraesCS7D01G071500 chr4A 87.097 155 19 1 3493 3647 649188692 649188845 1.350000e-39 174.0
13 TraesCS7D01G071500 chr4A 86.452 155 20 1 3493 3647 649156236 649156389 6.260000e-38 169.0
14 TraesCS7D01G071500 chr2B 91.858 3144 219 23 1 3118 783889643 783886511 0.000000e+00 4353.0
15 TraesCS7D01G071500 chr2B 87.629 970 107 10 1 967 784346520 784347479 0.000000e+00 1114.0
16 TraesCS7D01G071500 chr7A 91.199 3227 224 32 28 3224 41618775 41621971 0.000000e+00 4331.0
17 TraesCS7D01G071500 chrUn 91.525 59 4 1 3340 3398 250931640 250931583 3.020000e-11 80.5
18 TraesCS7D01G071500 chrUn 91.525 59 4 1 3340 3398 283092153 283092210 3.020000e-11 80.5
19 TraesCS7D01G071500 chrUn 91.525 59 4 1 3340 3398 370047749 370047692 3.020000e-11 80.5
20 TraesCS7D01G071500 chrUn 91.525 59 4 1 3340 3398 387612261 387612318 3.020000e-11 80.5
21 TraesCS7D01G071500 chrUn 91.525 59 4 1 3340 3398 387613941 387613998 3.020000e-11 80.5


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 TraesCS7D01G071500 chr7D 42081174 42084820 3646 True 6735 6735 100.0000 1 3647 1 chr7D.!!$R2 3646
1 TraesCS7D01G071500 chr7D 42212203 42215431 3228 False 4767 4767 93.3640 1 3224 1 chr7D.!!$F1 3223
2 TraesCS7D01G071500 chr7D 41914354 41917430 3076 True 4455 4455 92.8250 1 3079 1 chr7D.!!$R1 3078
3 TraesCS7D01G071500 chr7B 2561379 2564600 3221 True 4669 4669 92.8400 1 3227 1 chr7B.!!$R1 3226
4 TraesCS7D01G071500 chr4A 657366548 657369754 3206 False 4602 4602 92.5700 1 3218 1 chr4A.!!$F7 3217
5 TraesCS7D01G071500 chr4A 649144380 649147598 3218 False 4597 4597 92.4980 1 3218 1 chr4A.!!$F3 3217
6 TraesCS7D01G071500 chr4A 657306853 657310063 3210 False 4590 4590 92.4790 1 3218 1 chr4A.!!$F6 3217
7 TraesCS7D01G071500 chr4A 649056789 649059487 2698 False 3616 3616 90.9630 532 3224 1 chr4A.!!$F1 2692
8 TraesCS7D01G071500 chr4A 649173854 649175929 2075 False 2931 2931 92.1640 1 2083 1 chr4A.!!$F5 2082
9 TraesCS7D01G071500 chr4A 649184120 649188845 4725 False 2039 3904 89.7765 471 3647 2 chr4A.!!$F8 3176
10 TraesCS7D01G071500 chr2B 783886511 783889643 3132 True 4353 4353 91.8580 1 3118 1 chr2B.!!$R1 3117
11 TraesCS7D01G071500 chr2B 784346520 784347479 959 False 1114 1114 87.6290 1 967 1 chr2B.!!$F1 966
12 TraesCS7D01G071500 chr7A 41618775 41621971 3196 False 4331 4331 91.1990 28 3224 1 chr7A.!!$F1 3196

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
959 996 0.036875 GCAAACACTCCAGCCTACCT 59.963 55.0 0.0 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2692 2756 1.633852 CTTGTTGAGGAGCTCAGCGC 61.634 60.0 17.19 0.0 43.08 5.92 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
63 65 1.270094 TGAGGTAGCAGAACCACAACG 60.270 52.381 5.79 0.00 42.40 4.10
92 94 4.617520 TCACGGCAGCGCAAAGGA 62.618 61.111 11.47 0.00 0.00 3.36
110 112 1.079127 ACGTGCCGAATAGCAGCTT 60.079 52.632 0.00 0.00 45.14 3.74
206 208 3.574396 TGCGGATGGAGTTTCTAGATAGG 59.426 47.826 0.00 0.00 0.00 2.57
221 223 2.239907 AGATAGGCAACCTGAGGAAACC 59.760 50.000 4.99 2.57 34.61 3.27
222 224 1.440618 TAGGCAACCTGAGGAAACCA 58.559 50.000 4.99 0.00 34.61 3.67
232 234 3.512724 CCTGAGGAAACCATTCAATGCTT 59.487 43.478 0.00 0.00 37.29 3.91
271 273 2.517402 GCAACCCGACCACCACAA 60.517 61.111 0.00 0.00 0.00 3.33
281 283 0.608035 ACCACCACAATGTAAGGCCG 60.608 55.000 0.00 0.00 0.00 6.13
381 383 3.567397 ACTAGCCATGACGGATTAGTCT 58.433 45.455 0.00 0.00 41.47 3.24
382 384 3.570550 ACTAGCCATGACGGATTAGTCTC 59.429 47.826 0.00 0.00 41.47 3.36
393 395 9.742144 ATGACGGATTAGTCTCTACAAGTATAT 57.258 33.333 0.00 0.00 41.47 0.86
461 464 6.749923 ACACTAGCAATCTTTCTTGAATCC 57.250 37.500 0.00 0.00 0.00 3.01
469 472 9.129532 AGCAATCTTTCTTGAATCCTAATTAGG 57.870 33.333 23.54 23.54 45.02 2.69
486 489 6.997942 AATTAGGATACAAGTACTCCCTCC 57.002 41.667 0.00 0.75 41.41 4.30
501 504 1.108776 CCTCCTCCCGAATTACGTCA 58.891 55.000 0.00 0.00 40.78 4.35
570 593 5.371526 AGATACATCCATTTCTGCGACAAT 58.628 37.500 0.00 0.00 0.00 2.71
573 596 7.663081 AGATACATCCATTTCTGCGACAATTAT 59.337 33.333 0.00 0.00 0.00 1.28
575 598 6.498304 ACATCCATTTCTGCGACAATTATTC 58.502 36.000 0.00 0.00 0.00 1.75
576 599 5.155509 TCCATTTCTGCGACAATTATTCG 57.844 39.130 4.62 4.62 39.56 3.34
746 778 4.762251 AGAGTGTGTTTCCTGCCTATTTTC 59.238 41.667 0.00 0.00 0.00 2.29
754 787 3.675613 TCCTGCCTATTTTCTATCCCCA 58.324 45.455 0.00 0.00 0.00 4.96
842 875 5.409826 CCAGGATAAGGCGTCAATAAATCTC 59.590 44.000 0.00 0.00 0.00 2.75
847 880 5.615925 AAGGCGTCAATAAATCTCTACCT 57.384 39.130 0.00 0.00 0.00 3.08
929 965 6.208797 CCACATATGCATCCAAAGATTCATCT 59.791 38.462 0.19 0.00 37.51 2.90
936 972 6.153170 TGCATCCAAAGATTCATCTAGCAAAA 59.847 34.615 0.00 0.00 35.76 2.44
959 996 0.036875 GCAAACACTCCAGCCTACCT 59.963 55.000 0.00 0.00 0.00 3.08
1155 1192 0.318275 CCTACGATCGCCTCAAGCTC 60.318 60.000 16.60 0.00 40.39 4.09
1324 1361 5.072055 AGTCATCCACATTTGACAATGACA 58.928 37.500 14.85 0.00 43.72 3.58
1467 1504 1.407258 CTGCAAAGTTTTCCGGGTGAA 59.593 47.619 0.00 0.00 0.00 3.18
1473 1510 4.360951 AAGTTTTCCGGGTGAAGTCATA 57.639 40.909 0.00 0.00 33.63 2.15
1600 1637 3.190327 TGGTGCCAATACTTCAATCGTTG 59.810 43.478 0.00 0.00 0.00 4.10
1681 1729 3.782443 CCACCTCCACCCTACGGC 61.782 72.222 0.00 0.00 0.00 5.68
1682 1730 3.000819 CACCTCCACCCTACGGCA 61.001 66.667 0.00 0.00 0.00 5.69
1683 1731 3.001406 ACCTCCACCCTACGGCAC 61.001 66.667 0.00 0.00 0.00 5.01
1684 1732 2.683933 CCTCCACCCTACGGCACT 60.684 66.667 0.00 0.00 0.00 4.40
1830 1885 6.141685 GCACAAACAACTAAACAATTAGACGG 59.858 38.462 2.80 0.00 40.90 4.79
2063 2121 3.961480 CCTATCGAGGTATGGCATCAA 57.039 47.619 1.65 0.00 38.16 2.57
2253 2311 9.650539 CAATATTCTATTCATCTCCTACAGGTG 57.349 37.037 0.00 0.00 33.97 4.00
2417 2475 9.119418 TGAATATGTCTGAGTTTGTTTTCTTGA 57.881 29.630 0.00 0.00 0.00 3.02
2618 2682 5.446709 CAAGAATATCGCCAATGACATCAC 58.553 41.667 0.00 0.00 0.00 3.06
2623 2687 2.709213 TCGCCAATGACATCACATCAA 58.291 42.857 0.00 0.00 0.00 2.57
2659 2723 7.581213 ATGTCCGGCTAAATTATCAAATCAA 57.419 32.000 0.00 0.00 0.00 2.57
2692 2756 1.970917 GACAACGCGATGCCTTCCAG 61.971 60.000 15.93 0.00 0.00 3.86
2698 2762 2.124983 GATGCCTTCCAGCGCTGA 60.125 61.111 38.06 21.04 34.65 4.26
2802 2866 2.224426 TGGGATGTCCACTGTGTTGTAC 60.224 50.000 7.08 0.58 41.46 2.90
2857 2921 4.076394 TGTAACTTTTCCCCATCCTTTCG 58.924 43.478 0.00 0.00 0.00 3.46
2892 2956 4.760227 CAAAGGTCTTTTGCGTTTTCTG 57.240 40.909 0.00 0.00 39.71 3.02
3034 3140 1.922447 AGGTTCATATGTGCCAGGGAA 59.078 47.619 16.48 0.00 0.00 3.97
3047 3153 4.036852 GTGCCAGGGAATAAGCATTACTTC 59.963 45.833 0.00 0.00 39.97 3.01
3110 3218 7.449934 AGAGCTTTGTAATTTTTGTTGAACG 57.550 32.000 0.00 0.00 0.00 3.95
3124 3232 7.982761 TTTGTTGAACGGTTACCTACAATAT 57.017 32.000 0.00 0.00 0.00 1.28
3191 3299 6.723298 ACATGATGTTTAACAACAAGGGAA 57.277 33.333 11.79 0.00 46.17 3.97
3229 3364 8.697507 ATACAATCCCAAATTATCAAGAGTCC 57.302 34.615 0.00 0.00 0.00 3.85
3230 3365 5.893824 ACAATCCCAAATTATCAAGAGTCCC 59.106 40.000 0.00 0.00 0.00 4.46
3231 3366 4.150897 TCCCAAATTATCAAGAGTCCCG 57.849 45.455 0.00 0.00 0.00 5.14
3232 3367 3.521937 TCCCAAATTATCAAGAGTCCCGT 59.478 43.478 0.00 0.00 0.00 5.28
3233 3368 4.018779 TCCCAAATTATCAAGAGTCCCGTT 60.019 41.667 0.00 0.00 0.00 4.44
3235 3370 5.163652 CCCAAATTATCAAGAGTCCCGTTTC 60.164 44.000 0.00 0.00 0.00 2.78
3237 3372 6.403636 CCAAATTATCAAGAGTCCCGTTTCAG 60.404 42.308 0.00 0.00 0.00 3.02
3238 3373 4.884668 TTATCAAGAGTCCCGTTTCAGT 57.115 40.909 0.00 0.00 0.00 3.41
3239 3374 5.988310 TTATCAAGAGTCCCGTTTCAGTA 57.012 39.130 0.00 0.00 0.00 2.74
3240 3375 3.655276 TCAAGAGTCCCGTTTCAGTAC 57.345 47.619 0.00 0.00 0.00 2.73
3241 3376 2.960384 TCAAGAGTCCCGTTTCAGTACA 59.040 45.455 0.00 0.00 0.00 2.90
3242 3377 3.057734 CAAGAGTCCCGTTTCAGTACAC 58.942 50.000 0.00 0.00 0.00 2.90
3243 3378 1.617357 AGAGTCCCGTTTCAGTACACC 59.383 52.381 0.00 0.00 0.00 4.16
3244 3379 0.683412 AGTCCCGTTTCAGTACACCC 59.317 55.000 0.00 0.00 0.00 4.61
3245 3380 0.321034 GTCCCGTTTCAGTACACCCC 60.321 60.000 0.00 0.00 0.00 4.95
3246 3381 1.002990 CCCGTTTCAGTACACCCCC 60.003 63.158 0.00 0.00 0.00 5.40
3248 3383 0.036671 CCGTTTCAGTACACCCCCTC 60.037 60.000 0.00 0.00 0.00 4.30
3251 3386 1.697982 GTTTCAGTACACCCCCTCACT 59.302 52.381 0.00 0.00 0.00 3.41
3252 3387 2.901839 GTTTCAGTACACCCCCTCACTA 59.098 50.000 0.00 0.00 0.00 2.74
3255 3390 2.901839 TCAGTACACCCCCTCACTAAAC 59.098 50.000 0.00 0.00 0.00 2.01
3256 3391 2.635915 CAGTACACCCCCTCACTAAACA 59.364 50.000 0.00 0.00 0.00 2.83
3268 3509 7.450903 CCCCTCACTAAACATATAAAGGGTAG 58.549 42.308 0.00 0.00 40.56 3.18
3278 3519 9.847224 AAACATATAAAGGGTAGTATGGACTTG 57.153 33.333 0.00 0.00 37.10 3.16
3279 3520 7.450903 ACATATAAAGGGTAGTATGGACTTGC 58.549 38.462 0.00 0.00 37.10 4.01
3289 3530 1.668419 ATGGACTTGCGCCTAATCAC 58.332 50.000 4.18 0.00 0.00 3.06
3290 3531 0.392461 TGGACTTGCGCCTAATCACC 60.392 55.000 4.18 0.00 0.00 4.02
3298 3539 1.334054 CGCCTAATCACCGTATACGC 58.666 55.000 19.86 1.81 38.18 4.42
3303 3544 4.470462 CCTAATCACCGTATACGCTGTAC 58.530 47.826 19.86 0.00 38.18 2.90
3305 3546 4.579454 AATCACCGTATACGCTGTACAT 57.421 40.909 19.86 3.86 38.18 2.29
3307 3548 2.033675 TCACCGTATACGCTGTACATGG 59.966 50.000 19.86 5.38 38.18 3.66
3311 3552 3.489444 CGTATACGCTGTACATGGCTAG 58.511 50.000 13.08 0.00 0.00 3.42
3330 3571 2.858745 AGTTTAGAAACGGGCACACAT 58.141 42.857 0.00 0.00 43.51 3.21
3332 3573 1.816074 TTAGAAACGGGCACACATCC 58.184 50.000 0.00 0.00 0.00 3.51
3333 3574 0.035820 TAGAAACGGGCACACATCCC 60.036 55.000 0.00 0.00 40.43 3.85
3339 3580 2.890474 GGCACACATCCCGCTACG 60.890 66.667 0.00 0.00 0.00 3.51
3343 3584 3.849951 CACATCCCGCTACGGCCT 61.850 66.667 0.00 0.00 46.86 5.19
3344 3585 3.849951 ACATCCCGCTACGGCCTG 61.850 66.667 0.00 2.74 46.86 4.85
3345 3586 4.609018 CATCCCGCTACGGCCTGG 62.609 72.222 0.00 0.00 46.86 4.45
3365 3606 3.843893 GGCTTGGCCCATTCATATTTT 57.156 42.857 0.00 0.00 44.06 1.82
3371 4047 6.183360 GCTTGGCCCATTCATATTTTCTTTTG 60.183 38.462 0.00 0.00 0.00 2.44
3374 4050 7.230027 TGGCCCATTCATATTTTCTTTTGTTT 58.770 30.769 0.00 0.00 0.00 2.83
3407 4083 1.636148 AAAATGAGCATGTGTGGGCT 58.364 45.000 0.00 0.00 44.48 5.19
3408 4084 1.636148 AAATGAGCATGTGTGGGCTT 58.364 45.000 0.00 0.00 41.22 4.35
3409 4085 0.892755 AATGAGCATGTGTGGGCTTG 59.107 50.000 0.00 0.00 41.22 4.01
3410 4086 0.968901 ATGAGCATGTGTGGGCTTGG 60.969 55.000 0.00 0.00 41.22 3.61
3411 4087 2.993264 AGCATGTGTGGGCTTGGC 60.993 61.111 0.00 0.00 36.92 4.52
3421 4097 3.087065 GGCTTGGCCCCTCACTAA 58.913 61.111 0.00 0.00 44.06 2.24
3422 4098 1.382629 GGCTTGGCCCCTCACTAAA 59.617 57.895 0.00 0.00 44.06 1.85
3423 4099 0.965866 GGCTTGGCCCCTCACTAAAC 60.966 60.000 0.00 0.00 44.06 2.01
3424 4100 1.305930 GCTTGGCCCCTCACTAAACG 61.306 60.000 0.00 0.00 0.00 3.60
3425 4101 0.036306 CTTGGCCCCTCACTAAACGT 59.964 55.000 0.00 0.00 0.00 3.99
3426 4102 1.276989 CTTGGCCCCTCACTAAACGTA 59.723 52.381 0.00 0.00 0.00 3.57
3427 4103 1.575419 TGGCCCCTCACTAAACGTAT 58.425 50.000 0.00 0.00 0.00 3.06
3429 4105 3.106054 TGGCCCCTCACTAAACGTATAA 58.894 45.455 0.00 0.00 0.00 0.98
3430 4106 3.518705 TGGCCCCTCACTAAACGTATAAA 59.481 43.478 0.00 0.00 0.00 1.40
3431 4107 4.124970 GGCCCCTCACTAAACGTATAAAG 58.875 47.826 0.00 0.00 0.00 1.85
3432 4108 4.124970 GCCCCTCACTAAACGTATAAAGG 58.875 47.826 0.00 0.00 0.00 3.11
3433 4109 4.700700 CCCCTCACTAAACGTATAAAGGG 58.299 47.826 11.67 11.67 41.61 3.95
3435 4111 5.363580 CCCCTCACTAAACGTATAAAGGGTA 59.636 44.000 15.42 0.00 40.56 3.69
3436 4112 6.462067 CCCCTCACTAAACGTATAAAGGGTAG 60.462 46.154 15.42 2.87 40.56 3.18
3441 4321 6.532657 CACTAAACGTATAAAGGGTAGTGTGG 59.467 42.308 0.00 0.00 33.26 4.17
3453 4333 3.558033 GGTAGTGTGGACTTTTTCCCAA 58.442 45.455 0.00 0.00 45.17 4.12
3455 4335 4.217767 GGTAGTGTGGACTTTTTCCCAATC 59.782 45.833 0.00 0.00 45.17 2.67
3456 4336 3.909732 AGTGTGGACTTTTTCCCAATCA 58.090 40.909 0.00 0.00 45.17 2.57
3457 4337 3.636764 AGTGTGGACTTTTTCCCAATCAC 59.363 43.478 0.00 0.00 45.17 3.06
3458 4338 2.962421 TGTGGACTTTTTCCCAATCACC 59.038 45.455 0.00 0.00 45.17 4.02
3460 4340 2.235891 GGACTTTTTCCCAATCACCGT 58.764 47.619 0.00 0.00 38.70 4.83
3462 4342 4.014406 GGACTTTTTCCCAATCACCGTAT 58.986 43.478 0.00 0.00 38.70 3.06
3463 4343 5.187687 GGACTTTTTCCCAATCACCGTATA 58.812 41.667 0.00 0.00 38.70 1.47
3464 4344 5.065602 GGACTTTTTCCCAATCACCGTATAC 59.934 44.000 0.00 0.00 38.70 1.47
3465 4345 5.562635 ACTTTTTCCCAATCACCGTATACA 58.437 37.500 3.32 0.00 0.00 2.29
3466 4346 5.413523 ACTTTTTCCCAATCACCGTATACAC 59.586 40.000 3.32 0.00 0.00 2.90
3468 4348 3.812156 TCCCAATCACCGTATACACTG 57.188 47.619 3.32 0.00 0.00 3.66
3470 4350 4.279982 TCCCAATCACCGTATACACTGTA 58.720 43.478 3.32 0.00 0.00 2.74
3473 4353 5.041287 CCAATCACCGTATACACTGTACAG 58.959 45.833 21.44 21.44 0.00 2.74
3474 4354 5.393787 CCAATCACCGTATACACTGTACAGT 60.394 44.000 22.95 22.95 43.61 3.55
3490 4370 8.311650 ACTGTACAGTGCTAGTTTAGAAAATG 57.688 34.615 27.41 0.00 40.75 2.32
3491 4371 7.095187 ACTGTACAGTGCTAGTTTAGAAAATGC 60.095 37.037 27.41 0.00 40.75 3.56
3527 5166 6.912051 GCCCATTCACATTTTCTTTTGTTTTC 59.088 34.615 0.00 0.00 0.00 2.29
3528 5167 7.414984 GCCCATTCACATTTTCTTTTGTTTTCA 60.415 33.333 0.00 0.00 0.00 2.69
3567 5206 4.814234 TGGGCATATGTACGTTTCAATCTC 59.186 41.667 4.29 0.00 0.00 2.75
3575 5214 5.227908 TGTACGTTTCAATCTCTCAACCTC 58.772 41.667 0.00 0.00 0.00 3.85
3585 5224 4.527509 TCTCTCAACCTCACAGATCAAC 57.472 45.455 0.00 0.00 0.00 3.18
3587 5226 4.219507 TCTCTCAACCTCACAGATCAACTC 59.780 45.833 0.00 0.00 0.00 3.01
3608 5247 3.087031 CAACTAGGACAACCTACTCGGA 58.913 50.000 0.00 0.00 45.83 4.55
3612 5251 0.245813 GGACAACCTACTCGGACACC 59.754 60.000 0.00 0.00 36.31 4.16
3616 5255 0.966920 AACCTACTCGGACACCACAG 59.033 55.000 0.00 0.00 36.31 3.66
3622 5261 0.732880 CTCGGACACCACAGCTTACG 60.733 60.000 0.00 0.00 0.00 3.18
3638 5277 3.911964 GCTTACGTGCCAATAAACTGTTG 59.088 43.478 0.00 0.00 0.00 3.33
3641 5280 6.615264 TTACGTGCCAATAAACTGTTGTTA 57.385 33.333 0.00 0.00 34.96 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.126863 TGTTTTGAGATCTGGTCCTATTGT 57.873 37.500 0.00 0.00 0.00 2.71
110 112 4.966965 TTGTTCCGCTTGTTCTTTTGTA 57.033 36.364 0.00 0.00 0.00 2.41
178 180 2.151202 GAAACTCCATCCGCAACAAGA 58.849 47.619 0.00 0.00 0.00 3.02
206 208 2.238521 TGAATGGTTTCCTCAGGTTGC 58.761 47.619 0.00 0.00 0.00 4.17
232 234 2.769663 ACTTGTACCACCTGTCTTGTCA 59.230 45.455 0.00 0.00 0.00 3.58
271 273 0.179045 GAGCATGGACGGCCTTACAT 60.179 55.000 9.82 0.00 34.31 2.29
281 283 2.871182 TGTACTGATCGAGCATGGAC 57.129 50.000 2.72 6.18 0.00 4.02
393 395 5.480642 TGCAAGCATTTATTTCCTTTCCA 57.519 34.783 0.00 0.00 0.00 3.53
461 464 7.951245 AGGAGGGAGTACTTGTATCCTAATTAG 59.049 40.741 14.68 5.43 33.99 1.73
469 472 3.232662 GGGAGGAGGGAGTACTTGTATC 58.767 54.545 0.00 0.00 0.00 2.24
484 487 2.380941 TCATGACGTAATTCGGGAGGA 58.619 47.619 0.00 0.00 44.69 3.71
486 489 5.501715 CATTTTCATGACGTAATTCGGGAG 58.498 41.667 0.00 0.00 44.69 4.30
570 593 0.261402 TACTCCCCCGTCCCGAATAA 59.739 55.000 0.00 0.00 0.00 1.40
573 596 0.178981 CTATACTCCCCCGTCCCGAA 60.179 60.000 0.00 0.00 0.00 4.30
575 598 0.892814 GTCTATACTCCCCCGTCCCG 60.893 65.000 0.00 0.00 0.00 5.14
576 599 0.482006 AGTCTATACTCCCCCGTCCC 59.518 60.000 0.00 0.00 0.00 4.46
628 655 7.787623 ATTTCTTTCCATTCCTCTTGTCATT 57.212 32.000 0.00 0.00 0.00 2.57
636 663 9.454859 TCTCTTTAGAATTTCTTTCCATTCCTC 57.545 33.333 3.86 0.00 34.67 3.71
671 698 6.358178 TCAACCGGCTTTGGATATGTTTATA 58.642 36.000 0.00 0.00 0.00 0.98
672 699 5.197451 TCAACCGGCTTTGGATATGTTTAT 58.803 37.500 0.00 0.00 0.00 1.40
746 778 7.257790 TGTCCTGATACATTATTGGGGATAG 57.742 40.000 0.00 0.00 0.00 2.08
754 787 7.557358 TGTGAAAGCATGTCCTGATACATTATT 59.443 33.333 0.00 0.00 38.01 1.40
789 822 9.542462 TGTACTAGTATTCCATCTAAACATTGC 57.458 33.333 5.75 0.00 0.00 3.56
794 827 8.472413 TGGTGTGTACTAGTATTCCATCTAAAC 58.528 37.037 5.75 0.00 0.00 2.01
900 936 1.401761 TTGGATGCATATGTGGGCAC 58.598 50.000 0.00 0.00 43.75 5.01
929 965 3.445450 TGGAGTGTTTGCTTGTTTTGCTA 59.555 39.130 0.00 0.00 0.00 3.49
936 972 0.106519 AGGCTGGAGTGTTTGCTTGT 60.107 50.000 0.00 0.00 0.00 3.16
959 996 0.105760 AGTTGTGGGATGGGTGCAAA 60.106 50.000 0.00 0.00 0.00 3.68
1053 1090 2.734755 ATTGGCTAAGGCATGCTACA 57.265 45.000 18.92 5.13 38.08 2.74
1055 1092 3.117926 TGAGAATTGGCTAAGGCATGCTA 60.118 43.478 18.92 1.67 38.08 3.49
1155 1192 4.701651 TCACATAACTCCTTTGCAAGATGG 59.298 41.667 0.00 4.07 0.00 3.51
1189 1226 2.743938 CGCATCTAGTGGGTATGACAC 58.256 52.381 0.00 0.00 39.10 3.67
1373 1410 2.689983 AGAAACTTTGCTGTGAACCTGG 59.310 45.455 0.00 0.00 0.00 4.45
1467 1504 4.344978 TGTAGCTTGAGGAGTGTATGACT 58.655 43.478 0.00 0.00 37.76 3.41
1473 1510 2.965831 TGACTTGTAGCTTGAGGAGTGT 59.034 45.455 0.00 0.00 0.00 3.55
1600 1637 3.695816 GTCTACATACCGGGTTTCGTAC 58.304 50.000 4.31 0.00 37.11 3.67
1607 1644 0.682209 AGTGCGTCTACATACCGGGT 60.682 55.000 6.32 4.46 0.00 5.28
1681 1729 6.542370 CCCTGTACCCACTGAAAATATAAGTG 59.458 42.308 0.00 0.00 40.81 3.16
1682 1730 6.659824 CCCTGTACCCACTGAAAATATAAGT 58.340 40.000 0.00 0.00 0.00 2.24
1683 1731 5.531287 GCCCTGTACCCACTGAAAATATAAG 59.469 44.000 0.00 0.00 0.00 1.73
1684 1732 5.044772 TGCCCTGTACCCACTGAAAATATAA 60.045 40.000 0.00 0.00 0.00 0.98
1800 1855 6.826893 ATTGTTTAGTTGTTTGTGCATGTC 57.173 33.333 0.00 0.00 0.00 3.06
2063 2121 1.813102 TGGACCCATTTTTGGCCTTT 58.187 45.000 3.32 0.00 0.00 3.11
2253 2311 3.071602 TGATCTTAGTAATGCTCCCCTGC 59.928 47.826 0.00 0.00 0.00 4.85
2267 2325 6.867550 TCAACTATATCGCCCATGATCTTAG 58.132 40.000 0.00 0.00 0.00 2.18
2417 2475 7.871973 TGTTAGCAGATTTAACAATTGTTGCAT 59.128 29.630 29.72 21.23 37.89 3.96
2618 2682 4.658713 GACATAGCGTCCATCATTGATG 57.341 45.455 18.00 18.00 38.85 3.07
2692 2756 1.633852 CTTGTTGAGGAGCTCAGCGC 61.634 60.000 17.19 0.00 43.08 5.92
2698 2762 2.909006 TCCTTGATCTTGTTGAGGAGCT 59.091 45.455 0.00 0.00 32.91 4.09
2857 2921 2.663119 GACCTTTGCGTTTCATTGCATC 59.337 45.455 0.00 0.00 41.42 3.91
3218 3353 4.768448 TGTACTGAAACGGGACTCTTGATA 59.232 41.667 0.00 0.00 0.00 2.15
3224 3359 1.337541 GGGTGTACTGAAACGGGACTC 60.338 57.143 0.00 0.00 0.00 3.36
3227 3362 1.482748 GGGGGTGTACTGAAACGGGA 61.483 60.000 0.00 0.00 0.00 5.14
3228 3363 1.002990 GGGGGTGTACTGAAACGGG 60.003 63.158 0.00 0.00 0.00 5.28
3229 3364 0.036671 GAGGGGGTGTACTGAAACGG 60.037 60.000 0.00 0.00 0.00 4.44
3230 3365 0.682852 TGAGGGGGTGTACTGAAACG 59.317 55.000 0.00 0.00 0.00 3.60
3231 3366 1.697982 AGTGAGGGGGTGTACTGAAAC 59.302 52.381 0.00 0.00 0.00 2.78
3232 3367 2.112279 AGTGAGGGGGTGTACTGAAA 57.888 50.000 0.00 0.00 0.00 2.69
3233 3368 3.263369 TTAGTGAGGGGGTGTACTGAA 57.737 47.619 0.00 0.00 0.00 3.02
3235 3370 2.635915 TGTTTAGTGAGGGGGTGTACTG 59.364 50.000 0.00 0.00 0.00 2.74
3237 3372 3.994931 ATGTTTAGTGAGGGGGTGTAC 57.005 47.619 0.00 0.00 0.00 2.90
3238 3373 7.147444 CCTTTATATGTTTAGTGAGGGGGTGTA 60.147 40.741 0.00 0.00 0.00 2.90
3239 3374 6.353602 CCTTTATATGTTTAGTGAGGGGGTGT 60.354 42.308 0.00 0.00 0.00 4.16
3240 3375 6.062095 CCTTTATATGTTTAGTGAGGGGGTG 58.938 44.000 0.00 0.00 0.00 4.61
3241 3376 5.133830 CCCTTTATATGTTTAGTGAGGGGGT 59.866 44.000 0.00 0.00 39.11 4.95
3242 3377 5.133830 ACCCTTTATATGTTTAGTGAGGGGG 59.866 44.000 9.67 0.00 45.46 5.40
3243 3378 6.262056 ACCCTTTATATGTTTAGTGAGGGG 57.738 41.667 9.67 0.00 45.46 4.79
3244 3379 8.030913 ACTACCCTTTATATGTTTAGTGAGGG 57.969 38.462 3.64 3.64 46.37 4.30
3252 3387 9.847224 CAAGTCCATACTACCCTTTATATGTTT 57.153 33.333 0.00 0.00 33.75 2.83
3255 3390 6.590292 CGCAAGTCCATACTACCCTTTATATG 59.410 42.308 0.00 0.00 33.75 1.78
3256 3391 6.698380 CGCAAGTCCATACTACCCTTTATAT 58.302 40.000 0.00 0.00 33.75 0.86
3278 3519 1.334054 CGTATACGGTGATTAGGCGC 58.666 55.000 17.61 0.00 35.37 6.53
3279 3520 1.334054 GCGTATACGGTGATTAGGCG 58.666 55.000 25.55 0.00 40.23 5.52
3289 3530 1.000607 AGCCATGTACAGCGTATACGG 60.001 52.381 25.55 13.02 40.23 4.02
3290 3531 2.417339 AGCCATGTACAGCGTATACG 57.583 50.000 20.87 20.87 43.27 3.06
3298 3539 5.291128 CCGTTTCTAAACTAGCCATGTACAG 59.709 44.000 0.33 0.00 36.77 2.74
3303 3544 2.354821 GCCCGTTTCTAAACTAGCCATG 59.645 50.000 4.24 0.00 36.77 3.66
3305 3546 1.348366 TGCCCGTTTCTAAACTAGCCA 59.652 47.619 11.69 0.25 36.77 4.75
3307 3548 2.159037 GTGTGCCCGTTTCTAAACTAGC 59.841 50.000 4.24 6.83 36.77 3.42
3311 3552 2.095415 GGATGTGTGCCCGTTTCTAAAC 60.095 50.000 0.00 0.00 35.59 2.01
3346 3587 4.677673 AGAAAATATGAATGGGCCAAGC 57.322 40.909 11.89 6.12 0.00 4.01
3348 3589 6.777782 ACAAAAGAAAATATGAATGGGCCAA 58.222 32.000 11.89 0.00 0.00 4.52
3349 3590 6.371595 ACAAAAGAAAATATGAATGGGCCA 57.628 33.333 9.61 9.61 0.00 5.36
3350 3591 7.686438 AAACAAAAGAAAATATGAATGGGCC 57.314 32.000 0.00 0.00 0.00 5.80
3392 4068 1.604308 CCAAGCCCACACATGCTCA 60.604 57.895 0.00 0.00 36.66 4.26
3393 4069 2.998279 GCCAAGCCCACACATGCTC 61.998 63.158 0.00 0.00 36.66 4.26
3395 4071 4.073200 GGCCAAGCCCACACATGC 62.073 66.667 0.00 0.00 44.06 4.06
3405 4081 1.305930 CGTTTAGTGAGGGGCCAAGC 61.306 60.000 4.39 0.00 0.00 4.01
3407 4083 1.350071 TACGTTTAGTGAGGGGCCAA 58.650 50.000 4.39 0.00 0.00 4.52
3408 4084 1.575419 ATACGTTTAGTGAGGGGCCA 58.425 50.000 4.39 0.00 0.00 5.36
3409 4085 3.825143 TTATACGTTTAGTGAGGGGCC 57.175 47.619 0.00 0.00 0.00 5.80
3410 4086 4.124970 CCTTTATACGTTTAGTGAGGGGC 58.875 47.826 0.00 0.00 0.00 5.80
3411 4087 4.162888 ACCCTTTATACGTTTAGTGAGGGG 59.837 45.833 22.71 14.47 40.91 4.79
3412 4088 5.349061 ACCCTTTATACGTTTAGTGAGGG 57.651 43.478 19.85 19.85 41.63 4.30
3413 4089 6.976925 CACTACCCTTTATACGTTTAGTGAGG 59.023 42.308 0.00 0.00 38.01 3.86
3419 4095 6.437162 AGTCCACACTACCCTTTATACGTTTA 59.563 38.462 0.00 0.00 0.00 2.01
3421 4097 4.774200 AGTCCACACTACCCTTTATACGTT 59.226 41.667 0.00 0.00 0.00 3.99
3422 4098 4.347607 AGTCCACACTACCCTTTATACGT 58.652 43.478 0.00 0.00 0.00 3.57
3423 4099 4.996788 AGTCCACACTACCCTTTATACG 57.003 45.455 0.00 0.00 0.00 3.06
3424 4100 7.120285 GGAAAAAGTCCACACTACCCTTTATAC 59.880 40.741 0.00 0.00 46.97 1.47
3425 4101 7.170277 GGAAAAAGTCCACACTACCCTTTATA 58.830 38.462 0.00 0.00 46.97 0.98
3426 4102 6.008331 GGAAAAAGTCCACACTACCCTTTAT 58.992 40.000 0.00 0.00 46.97 1.40
3427 4103 5.379187 GGAAAAAGTCCACACTACCCTTTA 58.621 41.667 0.00 0.00 46.97 1.85
3429 4105 3.828921 GGAAAAAGTCCACACTACCCTT 58.171 45.455 0.00 0.00 46.97 3.95
3430 4106 3.503800 GGAAAAAGTCCACACTACCCT 57.496 47.619 0.00 0.00 46.97 4.34
3441 4321 5.644636 TGTATACGGTGATTGGGAAAAAGTC 59.355 40.000 0.00 0.00 0.00 3.01
3465 4345 7.095187 GCATTTTCTAAACTAGCACTGTACAGT 60.095 37.037 22.95 22.95 43.61 3.55
3466 4346 7.237173 GCATTTTCTAAACTAGCACTGTACAG 58.763 38.462 21.44 21.44 0.00 2.74
3468 4348 6.403309 GGGCATTTTCTAAACTAGCACTGTAC 60.403 42.308 0.00 0.00 0.00 2.90
3470 4350 4.459337 GGGCATTTTCTAAACTAGCACTGT 59.541 41.667 0.00 0.00 0.00 3.55
3473 4353 4.142381 CCAGGGCATTTTCTAAACTAGCAC 60.142 45.833 0.00 0.00 0.00 4.40
3474 4354 4.016444 CCAGGGCATTTTCTAAACTAGCA 58.984 43.478 0.00 0.00 0.00 3.49
3475 4355 3.381590 CCCAGGGCATTTTCTAAACTAGC 59.618 47.826 0.00 0.00 0.00 3.42
3550 5189 6.931838 AGGTTGAGAGATTGAAACGTACATA 58.068 36.000 0.00 0.00 0.00 2.29
3551 5190 5.794894 AGGTTGAGAGATTGAAACGTACAT 58.205 37.500 0.00 0.00 0.00 2.29
3552 5191 5.209818 AGGTTGAGAGATTGAAACGTACA 57.790 39.130 0.00 0.00 0.00 2.90
3556 5195 4.058124 TGTGAGGTTGAGAGATTGAAACG 58.942 43.478 0.00 0.00 0.00 3.60
3560 5199 4.774200 TGATCTGTGAGGTTGAGAGATTGA 59.226 41.667 0.00 0.00 0.00 2.57
3567 5206 4.263018 TGAGTTGATCTGTGAGGTTGAG 57.737 45.455 0.00 0.00 0.00 3.02
3575 5214 5.139435 TGTCCTAGTTGAGTTGATCTGTG 57.861 43.478 0.00 0.00 0.00 3.66
3585 5224 3.128938 CCGAGTAGGTTGTCCTAGTTGAG 59.871 52.174 14.56 5.92 46.63 3.02
3587 5226 3.087031 TCCGAGTAGGTTGTCCTAGTTG 58.913 50.000 8.60 8.60 46.55 3.16
3601 5240 1.542915 GTAAGCTGTGGTGTCCGAGTA 59.457 52.381 0.00 0.00 0.00 2.59
3608 5247 1.597027 GGCACGTAAGCTGTGGTGT 60.597 57.895 11.47 0.00 45.62 4.16
3612 5251 3.188460 AGTTTATTGGCACGTAAGCTGTG 59.812 43.478 7.19 0.00 45.62 3.66
3616 5255 3.824414 ACAGTTTATTGGCACGTAAGC 57.176 42.857 0.00 0.00 45.62 3.09
3622 5261 5.240844 AGAGGTAACAACAGTTTATTGGCAC 59.759 40.000 0.00 0.00 41.41 5.01


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

AutoCloner maintained by Alex Coulton.