Multiple sequence alignment - TraesCS5D01G059400

Loading Multiple Alignment...

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 TraesCS5D01G059400 chr5D 100.000 4469 0 0 1 4469 56129577 56125109 0.000000e+00 8253.0
1 TraesCS5D01G059400 chr5D 95.652 46 0 2 3893 3938 381914444 381914487 6.200000e-09 73.1
2 TraesCS5D01G059400 chr5B 95.303 2853 115 9 1030 3866 58898318 58895469 0.000000e+00 4508.0
3 TraesCS5D01G059400 chr5B 87.262 840 60 28 214 1036 58899172 58898363 0.000000e+00 915.0
4 TraesCS5D01G059400 chr5B 92.986 442 27 3 4030 4469 58895157 58894718 3.770000e-180 641.0
5 TraesCS5D01G059400 chr5B 99.099 111 1 0 3938 4048 58895447 58895337 2.730000e-47 200.0
6 TraesCS5D01G059400 chr5B 82.278 158 21 7 7 160 504175831 504175985 3.630000e-26 130.0
7 TraesCS5D01G059400 chr5A 95.280 2055 89 4 1810 3859 44950820 44948769 0.000000e+00 3251.0
8 TraesCS5D01G059400 chr5A 90.424 1274 72 16 575 1820 44952410 44951159 0.000000e+00 1631.0
9 TraesCS5D01G059400 chr5A 92.483 572 31 9 3900 4469 44948769 44948208 0.000000e+00 808.0
10 TraesCS5D01G059400 chr2D 86.676 2837 308 43 1031 3822 112874023 112871212 0.000000e+00 3081.0
11 TraesCS5D01G059400 chr2D 91.071 56 3 2 303 357 377109311 377109257 1.720000e-09 75.0
12 TraesCS5D01G059400 chr2D 82.558 86 8 4 273 355 526927500 526927419 8.020000e-08 69.4
13 TraesCS5D01G059400 chr3B 86.261 2875 318 43 1031 3861 103243429 103246270 0.000000e+00 3049.0
14 TraesCS5D01G059400 chr2A 86.202 2870 323 44 1031 3858 114313479 114310641 0.000000e+00 3038.0
15 TraesCS5D01G059400 chr2A 90.769 65 4 1 3875 3937 675304193 675304129 7.960000e-13 86.1
16 TraesCS5D01G059400 chr2B 83.521 1954 273 30 1031 2948 163323611 163321671 0.000000e+00 1779.0
17 TraesCS5D01G059400 chr2B 83.315 887 108 27 2945 3824 163260464 163259611 0.000000e+00 782.0
18 TraesCS5D01G059400 chr2B 93.651 63 4 0 3876 3938 587169323 587169385 1.320000e-15 95.3
19 TraesCS5D01G059400 chrUn 90.686 408 38 0 2161 2568 477841090 477840683 1.090000e-150 544.0
20 TraesCS5D01G059400 chrUn 100.000 31 0 0 3871 3901 331535935 331535905 1.740000e-04 58.4
21 TraesCS5D01G059400 chrUn 100.000 31 0 0 3871 3901 331539260 331539290 1.740000e-04 58.4
22 TraesCS5D01G059400 chrUn 100.000 31 0 0 3871 3901 413738614 413738584 1.740000e-04 58.4
23 TraesCS5D01G059400 chr7B 89.706 68 1 1 3877 3938 537165956 537165889 1.030000e-11 82.4
24 TraesCS5D01G059400 chr7A 89.706 68 1 1 3877 3938 579340207 579340274 1.030000e-11 82.4
25 TraesCS5D01G059400 chr7A 88.710 62 3 2 3874 3935 210853587 210853644 6.200000e-09 73.1
26 TraesCS5D01G059400 chr4B 95.745 47 0 2 3894 3938 70256679 70256633 1.720000e-09 75.0
27 TraesCS5D01G059400 chr7D 88.710 62 3 2 3874 3935 156217708 156217765 6.200000e-09 73.1


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 TraesCS5D01G059400 chr5D 56125109 56129577 4468 True 8253.000000 8253 100.0000 1 4469 1 chr5D.!!$R1 4468
1 TraesCS5D01G059400 chr5B 58894718 58899172 4454 True 1566.000000 4508 93.6625 214 4469 4 chr5B.!!$R1 4255
2 TraesCS5D01G059400 chr5A 44948208 44952410 4202 True 1896.666667 3251 92.7290 575 4469 3 chr5A.!!$R1 3894
3 TraesCS5D01G059400 chr2D 112871212 112874023 2811 True 3081.000000 3081 86.6760 1031 3822 1 chr2D.!!$R1 2791
4 TraesCS5D01G059400 chr3B 103243429 103246270 2841 False 3049.000000 3049 86.2610 1031 3861 1 chr3B.!!$F1 2830
5 TraesCS5D01G059400 chr2A 114310641 114313479 2838 True 3038.000000 3038 86.2020 1031 3858 1 chr2A.!!$R1 2827
6 TraesCS5D01G059400 chr2B 163321671 163323611 1940 True 1779.000000 1779 83.5210 1031 2948 1 chr2B.!!$R2 1917
7 TraesCS5D01G059400 chr2B 163259611 163260464 853 True 782.000000 782 83.3150 2945 3824 1 chr2B.!!$R1 879

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
956 973 0.036306 CTGCCCTGAAACCCTACGTT 59.964 55.000 0.00 0.0 35.70 3.99 F
1395 1511 0.397816 AGGAGAAGGAGCGGCAGTAT 60.398 55.000 1.45 0.0 0.00 2.12 F
1718 1837 1.152830 GGTGGTCCAAGAAGGCCAA 59.847 57.895 5.01 0.0 42.62 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 2351 0.249155 CATTGGCACATCATTCGCCC 60.249 55.000 0.00 0.00 45.63 6.13 R
2375 2843 0.320771 CACCTCGCTAACCAGCTGTT 60.321 55.000 13.81 9.63 46.26 3.16 R
3509 3980 1.272490 TGAAGACTTCTACACAGCGGG 59.728 52.381 16.02 0.00 0.00 6.13 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
106 107 9.684448 CACAATTTACATTTTGTGTATACACCA 57.316 29.630 28.67 18.21 44.79 4.17
107 108 9.906660 ACAATTTACATTTTGTGTATACACCAG 57.093 29.630 28.67 17.28 45.88 4.00
108 109 9.352784 CAATTTACATTTTGTGTATACACCAGG 57.647 33.333 28.67 18.07 45.88 4.45
109 110 8.871629 ATTTACATTTTGTGTATACACCAGGA 57.128 30.769 28.67 14.91 45.88 3.86
110 111 8.693120 TTTACATTTTGTGTATACACCAGGAA 57.307 30.769 28.67 18.67 45.88 3.36
111 112 6.569179 ACATTTTGTGTATACACCAGGAAC 57.431 37.500 28.67 6.95 45.88 3.62
112 113 6.065374 ACATTTTGTGTATACACCAGGAACA 58.935 36.000 28.67 12.80 45.88 3.18
113 114 6.719370 ACATTTTGTGTATACACCAGGAACAT 59.281 34.615 28.67 14.26 45.88 2.71
114 115 7.232534 ACATTTTGTGTATACACCAGGAACATT 59.767 33.333 28.67 6.42 45.88 2.71
115 116 7.589958 TTTTGTGTATACACCAGGAACATTT 57.410 32.000 28.67 0.00 45.88 2.32
116 117 7.589958 TTTGTGTATACACCAGGAACATTTT 57.410 32.000 28.67 0.00 45.88 1.82
117 118 7.589958 TTGTGTATACACCAGGAACATTTTT 57.410 32.000 28.67 0.00 45.88 1.94
118 119 8.693120 TTGTGTATACACCAGGAACATTTTTA 57.307 30.769 28.67 6.23 45.88 1.52
119 120 8.871629 TGTGTATACACCAGGAACATTTTTAT 57.128 30.769 28.67 0.00 45.88 1.40
120 121 9.303116 TGTGTATACACCAGGAACATTTTTATT 57.697 29.630 28.67 0.00 45.88 1.40
127 128 9.088987 ACACCAGGAACATTTTTATTTAGATGT 57.911 29.630 0.00 0.00 34.41 3.06
128 129 9.927668 CACCAGGAACATTTTTATTTAGATGTT 57.072 29.630 0.00 0.66 43.29 2.71
148 149 9.859427 AGATGTTTAACAATGTCCAAATACATG 57.141 29.630 0.66 0.00 39.98 3.21
149 150 9.853555 GATGTTTAACAATGTCCAAATACATGA 57.146 29.630 0.66 0.00 39.98 3.07
191 192 9.319143 TGTTTACTTTTTCCCATACACAATTTG 57.681 29.630 0.00 0.00 0.00 2.32
192 193 7.954788 TTACTTTTTCCCATACACAATTTGC 57.045 32.000 0.00 0.00 0.00 3.68
193 194 5.923204 ACTTTTTCCCATACACAATTTGCA 58.077 33.333 0.00 0.00 0.00 4.08
194 195 6.532826 ACTTTTTCCCATACACAATTTGCAT 58.467 32.000 0.00 0.00 0.00 3.96
195 196 6.997476 ACTTTTTCCCATACACAATTTGCATT 59.003 30.769 0.00 0.00 0.00 3.56
196 197 7.501892 ACTTTTTCCCATACACAATTTGCATTT 59.498 29.630 0.00 0.00 0.00 2.32
197 198 7.814264 TTTTCCCATACACAATTTGCATTTT 57.186 28.000 0.00 0.00 0.00 1.82
198 199 7.814264 TTTCCCATACACAATTTGCATTTTT 57.186 28.000 0.00 0.00 0.00 1.94
273 274 9.971922 ATTCAGAAAAATTTGAGAACTTACCTG 57.028 29.630 0.00 0.00 0.00 4.00
285 286 9.924650 TTGAGAACTTACCTGTTTTATCTCTAC 57.075 33.333 0.00 0.00 0.00 2.59
298 305 9.146984 TGTTTTATCTCTACTTTTCCATACACG 57.853 33.333 0.00 0.00 0.00 4.49
300 307 8.922058 TTTATCTCTACTTTTCCATACACGTC 57.078 34.615 0.00 0.00 0.00 4.34
304 311 5.631026 TCTACTTTTCCATACACGTCGTAC 58.369 41.667 0.00 0.00 31.27 3.67
305 312 4.241590 ACTTTTCCATACACGTCGTACA 57.758 40.909 0.00 0.00 31.27 2.90
308 315 5.697633 ACTTTTCCATACACGTCGTACATTT 59.302 36.000 0.00 0.00 31.27 2.32
333 340 8.586570 TTTTGTGTACATGACAATCCATTTTC 57.413 30.769 0.00 0.00 40.66 2.29
335 342 8.628630 TTGTGTACATGACAATCCATTTTCTA 57.371 30.769 0.00 0.00 40.66 2.10
476 485 5.655893 AAACGGATGCAAAAATGTGAAAG 57.344 34.783 0.00 0.00 0.00 2.62
479 488 4.984161 ACGGATGCAAAAATGTGAAAGAAG 59.016 37.500 0.00 0.00 0.00 2.85
486 495 5.518487 GCAAAAATGTGAAAGAAGAAACGGA 59.482 36.000 0.00 0.00 0.00 4.69
491 500 6.693315 ATGTGAAAGAAGAAACGGAAGAAA 57.307 33.333 0.00 0.00 0.00 2.52
492 501 6.119144 TGTGAAAGAAGAAACGGAAGAAAG 57.881 37.500 0.00 0.00 0.00 2.62
493 502 5.065988 TGTGAAAGAAGAAACGGAAGAAAGG 59.934 40.000 0.00 0.00 0.00 3.11
497 506 5.752892 AGAAGAAACGGAAGAAAGGAAAC 57.247 39.130 0.00 0.00 0.00 2.78
570 581 5.963594 AGGTCGGTAATACTCAAGTCTTTC 58.036 41.667 0.00 0.00 0.00 2.62
573 584 6.154445 GTCGGTAATACTCAAGTCTTTCACA 58.846 40.000 0.00 0.00 0.00 3.58
863 879 1.066587 GCAGCGAGGTAGTAGGCAG 59.933 63.158 0.00 0.00 0.00 4.85
864 880 1.736586 CAGCGAGGTAGTAGGCAGG 59.263 63.158 0.00 0.00 0.00 4.85
865 881 1.455959 AGCGAGGTAGTAGGCAGGG 60.456 63.158 0.00 0.00 0.00 4.45
866 882 3.130227 CGAGGTAGTAGGCAGGGC 58.870 66.667 0.00 0.00 0.00 5.19
867 883 1.756950 CGAGGTAGTAGGCAGGGCA 60.757 63.158 0.00 0.00 0.00 5.36
887 903 1.452108 CGCCATCCCTTCCCACTTC 60.452 63.158 0.00 0.00 0.00 3.01
954 971 0.391263 GTCTGCCCTGAAACCCTACG 60.391 60.000 0.00 0.00 0.00 3.51
955 972 0.834687 TCTGCCCTGAAACCCTACGT 60.835 55.000 0.00 0.00 0.00 3.57
956 973 0.036306 CTGCCCTGAAACCCTACGTT 59.964 55.000 0.00 0.00 35.70 3.99
958 975 1.133730 TGCCCTGAAACCCTACGTTTT 60.134 47.619 0.00 0.00 44.88 2.43
971 988 5.105269 ACCCTACGTTTTGTTTTGATTTGGT 60.105 36.000 0.00 0.00 0.00 3.67
974 991 5.771602 ACGTTTTGTTTTGATTTGGTGAC 57.228 34.783 0.00 0.00 0.00 3.67
1013 1045 4.554036 GGCCATGGAGGAGGACGC 62.554 72.222 18.40 0.00 41.22 5.19
1014 1046 4.899239 GCCATGGAGGAGGACGCG 62.899 72.222 18.40 3.53 41.22 6.01
1015 1047 4.227134 CCATGGAGGAGGACGCGG 62.227 72.222 12.47 0.00 41.22 6.46
1016 1048 3.147595 CATGGAGGAGGACGCGGA 61.148 66.667 12.47 0.00 0.00 5.54
1017 1049 2.835431 ATGGAGGAGGACGCGGAG 60.835 66.667 12.47 0.00 0.00 4.63
1046 1114 1.740905 GCTTCTACTACGAGGGCCC 59.259 63.158 16.46 16.46 0.00 5.80
1115 1189 2.829458 CGAGGGGGACTCCGACTC 60.829 72.222 7.33 7.33 43.57 3.36
1119 1193 3.139469 GGGGACTCCGACTCCGAC 61.139 72.222 0.00 0.00 38.22 4.79
1134 1208 1.427592 CCGACTACGACTCCGAGGAC 61.428 65.000 0.00 0.00 42.66 3.85
1242 1337 2.610859 GAGGGGGTGGAGCAGGAA 60.611 66.667 0.00 0.00 0.00 3.36
1315 1431 2.359404 GGGAGGACACGGAGGAGA 59.641 66.667 0.00 0.00 0.00 3.71
1393 1509 2.284258 AGGAGAAGGAGCGGCAGT 60.284 61.111 1.45 0.00 0.00 4.40
1395 1511 0.397816 AGGAGAAGGAGCGGCAGTAT 60.398 55.000 1.45 0.00 0.00 2.12
1433 1552 4.812476 CCAAGCGTCATCGGCCGA 62.812 66.667 33.12 33.12 37.56 5.54
1505 1624 2.808202 CGAAGGTGGCTAAGATGATGGG 60.808 54.545 0.00 0.00 0.00 4.00
1718 1837 1.152830 GGTGGTCCAAGAAGGCCAA 59.847 57.895 5.01 0.00 42.62 4.52
1883 2351 2.502947 TCAGTGATGAACAGGAGATGGG 59.497 50.000 0.00 0.00 0.00 4.00
1993 2461 3.385384 TGCGACAGGAGCAGGAGG 61.385 66.667 0.00 0.00 40.01 4.30
2301 2769 1.522668 TTGGCTTGGAAGTCATGTCG 58.477 50.000 0.00 0.00 40.84 4.35
2375 2843 5.314718 ACTGAATCAATGGCTCCATATGA 57.685 39.130 3.65 8.56 35.31 2.15
2632 3103 1.726533 GCCGACTCTAGGACGAAGGG 61.727 65.000 0.00 0.00 0.00 3.95
2658 3129 3.827302 AGACCTTGTGTGACTCTATTCGT 59.173 43.478 0.00 0.00 0.00 3.85
2745 3216 3.947834 CTCCATGGAAGGGTGTATTTGAC 59.052 47.826 17.00 0.00 40.01 3.18
3051 3522 0.458716 TCGCCAATGAACGCATACGA 60.459 50.000 0.00 0.00 43.93 3.43
3133 3604 1.707427 AGCCAGTGACAAGGGAGAATT 59.293 47.619 0.00 0.00 0.00 2.17
3189 3660 1.899534 TGCAGCACAGCAAGCATCA 60.900 52.632 0.00 0.00 42.46 3.07
3206 3677 3.187227 GCATCACAATACCCAGCTTATCG 59.813 47.826 0.00 0.00 0.00 2.92
3360 3831 4.461081 GGCTCCGTGAGTATCTTCATAGAT 59.539 45.833 3.38 0.00 43.51 1.98
3513 3984 7.826260 TTTCATTTCATTTCTATTTTCCCGC 57.174 32.000 0.00 0.00 0.00 6.13
3514 3985 6.773976 TCATTTCATTTCTATTTTCCCGCT 57.226 33.333 0.00 0.00 0.00 5.52
3515 3986 6.563422 TCATTTCATTTCTATTTTCCCGCTG 58.437 36.000 0.00 0.00 0.00 5.18
3658 4131 3.444742 TGTTGCTGCCCAAGAATGAATAG 59.555 43.478 0.00 0.00 33.21 1.73
3721 4202 8.842358 ACTCCGTATTTGTTTATTTCTTGAGA 57.158 30.769 0.00 0.00 0.00 3.27
3741 4222 9.965824 CTTGAGATTTACTGTTGTTTTGGTAAT 57.034 29.630 0.00 0.00 0.00 1.89
3750 4231 8.432110 ACTGTTGTTTTGGTAATTTCATTTCC 57.568 30.769 0.00 0.00 0.00 3.13
3787 4270 3.141398 CATAATCGAATGTCCCCCACTG 58.859 50.000 0.00 0.00 0.00 3.66
3866 4349 4.263435 CTCCGATATGTACTACTCCCTCC 58.737 52.174 0.00 0.00 0.00 4.30
3868 4351 3.307269 CCGATATGTACTACTCCCTCCGA 60.307 52.174 0.00 0.00 0.00 4.55
3869 4352 4.515361 CGATATGTACTACTCCCTCCGAT 58.485 47.826 0.00 0.00 0.00 4.18
3871 4354 6.289834 CGATATGTACTACTCCCTCCGATAT 58.710 44.000 0.00 0.00 0.00 1.63
3872 4355 6.203145 CGATATGTACTACTCCCTCCGATATG 59.797 46.154 0.00 0.00 0.00 1.78
3873 4356 4.719026 TGTACTACTCCCTCCGATATGT 57.281 45.455 0.00 0.00 0.00 2.29
3875 4358 5.555017 TGTACTACTCCCTCCGATATGTAC 58.445 45.833 0.00 0.00 0.00 2.90
3876 4359 4.997545 ACTACTCCCTCCGATATGTACT 57.002 45.455 0.00 0.00 0.00 2.73
3878 4361 5.803552 ACTACTCCCTCCGATATGTACTAC 58.196 45.833 0.00 0.00 0.00 2.73
3879 4362 4.997545 ACTCCCTCCGATATGTACTACT 57.002 45.455 0.00 0.00 0.00 2.57
3880 4363 4.909001 ACTCCCTCCGATATGTACTACTC 58.091 47.826 0.00 0.00 0.00 2.59
3881 4364 4.263418 ACTCCCTCCGATATGTACTACTCC 60.263 50.000 0.00 0.00 0.00 3.85
3882 4365 3.009916 TCCCTCCGATATGTACTACTCCC 59.990 52.174 0.00 0.00 0.00 4.30
3883 4366 3.010361 CCCTCCGATATGTACTACTCCCT 59.990 52.174 0.00 0.00 0.00 4.20
3884 4367 4.263435 CCTCCGATATGTACTACTCCCTC 58.737 52.174 0.00 0.00 0.00 4.30
3885 4368 4.019141 CCTCCGATATGTACTACTCCCTCT 60.019 50.000 0.00 0.00 0.00 3.69
3886 4369 4.907809 TCCGATATGTACTACTCCCTCTG 58.092 47.826 0.00 0.00 0.00 3.35
3887 4370 4.350225 TCCGATATGTACTACTCCCTCTGT 59.650 45.833 0.00 0.00 0.00 3.41
3888 4371 5.545335 TCCGATATGTACTACTCCCTCTGTA 59.455 44.000 0.00 0.00 0.00 2.74
3889 4372 6.043590 TCCGATATGTACTACTCCCTCTGTAA 59.956 42.308 0.00 0.00 0.00 2.41
3890 4373 6.713903 CCGATATGTACTACTCCCTCTGTAAA 59.286 42.308 0.00 0.00 0.00 2.01
3891 4374 7.308469 CCGATATGTACTACTCCCTCTGTAAAC 60.308 44.444 0.00 0.00 0.00 2.01
3892 4375 7.228108 CGATATGTACTACTCCCTCTGTAAACA 59.772 40.741 0.00 0.00 0.00 2.83
3893 4376 8.834004 ATATGTACTACTCCCTCTGTAAACAA 57.166 34.615 0.00 0.00 0.00 2.83
3894 4377 6.982160 TGTACTACTCCCTCTGTAAACAAA 57.018 37.500 0.00 0.00 0.00 2.83
3895 4378 7.549147 TGTACTACTCCCTCTGTAAACAAAT 57.451 36.000 0.00 0.00 0.00 2.32
3896 4379 7.383687 TGTACTACTCCCTCTGTAAACAAATG 58.616 38.462 0.00 0.00 0.00 2.32
3897 4380 6.435292 ACTACTCCCTCTGTAAACAAATGT 57.565 37.500 0.00 0.00 0.00 2.71
3898 4381 7.549147 ACTACTCCCTCTGTAAACAAATGTA 57.451 36.000 0.00 0.00 0.00 2.29
3933 4416 6.780706 ACGTCTTACATTTGTTTACAGAGG 57.219 37.500 0.00 0.00 0.00 3.69
3934 4417 5.699458 ACGTCTTACATTTGTTTACAGAGGG 59.301 40.000 0.00 0.00 0.00 4.30
3935 4418 5.929992 CGTCTTACATTTGTTTACAGAGGGA 59.070 40.000 0.00 0.00 0.00 4.20
3936 4419 6.090898 CGTCTTACATTTGTTTACAGAGGGAG 59.909 42.308 0.00 0.00 0.00 4.30
4053 4734 7.119992 TGACAGCAAGTACTTTTGTTTAACTCA 59.880 33.333 18.62 11.03 0.00 3.41
4194 4876 4.265320 GCTTTTCAGTGTTTTGAAGGTTCG 59.735 41.667 0.00 0.00 38.25 3.95
4233 4915 5.489792 TTCAGTGTTGAGCTTCCTCTTAT 57.510 39.130 0.00 0.00 38.93 1.73
4234 4916 6.605471 TTCAGTGTTGAGCTTCCTCTTATA 57.395 37.500 0.00 0.00 38.93 0.98
4235 4917 6.605471 TCAGTGTTGAGCTTCCTCTTATAA 57.395 37.500 0.00 0.00 38.93 0.98
4236 4918 6.634805 TCAGTGTTGAGCTTCCTCTTATAAG 58.365 40.000 6.11 6.11 38.93 1.73
4237 4919 5.814705 CAGTGTTGAGCTTCCTCTTATAAGG 59.185 44.000 12.54 0.00 38.93 2.69
4240 4922 7.565398 AGTGTTGAGCTTCCTCTTATAAGGATA 59.435 37.037 12.54 0.00 44.87 2.59
4289 4971 5.548056 TGGTTCCTCTTAGATTCAAGACCTT 59.452 40.000 0.00 0.00 31.34 3.50
4362 5044 9.567848 CACTTGTTTCAGTTTACAGTTTATTGT 57.432 29.630 0.00 0.00 35.09 2.71
4396 5078 7.068702 TCCCCAATAATCTGCTGATGTATTTT 58.931 34.615 6.88 0.00 32.44 1.82
4406 5088 8.131455 TCTGCTGATGTATTTTATCGAAAGAC 57.869 34.615 0.00 0.00 46.97 3.01
4441 5123 5.865552 CAGTTTGAGTTATTGGCATTTCAGG 59.134 40.000 0.00 0.00 0.00 3.86
4448 5130 2.094100 TTGGCATTTCAGGGTGGAAA 57.906 45.000 0.00 0.00 40.72 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 9.906660 CTGGTGTATACACAAAATGTAAATTGT 57.093 29.630 31.52 0.00 46.90 2.71
82 83 9.352784 CCTGGTGTATACACAAAATGTAAATTG 57.647 33.333 31.52 9.51 46.90 2.32
83 84 9.303116 TCCTGGTGTATACACAAAATGTAAATT 57.697 29.630 31.52 0.00 46.90 1.82
84 85 8.871629 TCCTGGTGTATACACAAAATGTAAAT 57.128 30.769 31.52 0.00 46.90 1.40
85 86 8.569641 GTTCCTGGTGTATACACAAAATGTAAA 58.430 33.333 31.52 14.52 46.90 2.01
86 87 7.720074 TGTTCCTGGTGTATACACAAAATGTAA 59.280 33.333 31.52 15.82 46.90 2.41
101 102 9.088987 ACATCTAAATAAAAATGTTCCTGGTGT 57.911 29.630 0.00 0.00 0.00 4.16
102 103 9.927668 AACATCTAAATAAAAATGTTCCTGGTG 57.072 29.630 0.00 0.00 37.72 4.17
122 123 9.859427 CATGTATTTGGACATTGTTAAACATCT 57.141 29.630 0.00 0.00 37.99 2.90
123 124 9.853555 TCATGTATTTGGACATTGTTAAACATC 57.146 29.630 0.00 0.00 37.99 3.06
165 166 9.319143 CAAATTGTGTATGGGAAAAAGTAAACA 57.681 29.630 0.00 0.00 0.00 2.83
166 167 8.279800 GCAAATTGTGTATGGGAAAAAGTAAAC 58.720 33.333 0.00 0.00 0.00 2.01
167 168 7.987458 TGCAAATTGTGTATGGGAAAAAGTAAA 59.013 29.630 0.00 0.00 0.00 2.01
168 169 7.500992 TGCAAATTGTGTATGGGAAAAAGTAA 58.499 30.769 0.00 0.00 0.00 2.24
169 170 7.055667 TGCAAATTGTGTATGGGAAAAAGTA 57.944 32.000 0.00 0.00 0.00 2.24
170 171 5.923204 TGCAAATTGTGTATGGGAAAAAGT 58.077 33.333 0.00 0.00 0.00 2.66
171 172 7.437793 AATGCAAATTGTGTATGGGAAAAAG 57.562 32.000 0.00 0.00 32.17 2.27
172 173 7.814264 AAATGCAAATTGTGTATGGGAAAAA 57.186 28.000 0.00 0.00 32.17 1.94
173 174 7.814264 AAAATGCAAATTGTGTATGGGAAAA 57.186 28.000 0.00 0.00 32.17 2.29
174 175 7.814264 AAAAATGCAAATTGTGTATGGGAAA 57.186 28.000 0.00 0.00 32.17 3.13
247 248 9.971922 CAGGTAAGTTCTCAAATTTTTCTGAAT 57.028 29.630 0.00 0.00 0.00 2.57
266 267 9.720769 TGGAAAAGTAGAGATAAAACAGGTAAG 57.279 33.333 0.00 0.00 0.00 2.34
269 270 9.668497 GTATGGAAAAGTAGAGATAAAACAGGT 57.332 33.333 0.00 0.00 0.00 4.00
270 271 9.667107 TGTATGGAAAAGTAGAGATAAAACAGG 57.333 33.333 0.00 0.00 0.00 4.00
272 273 9.146984 CGTGTATGGAAAAGTAGAGATAAAACA 57.853 33.333 0.00 0.00 0.00 2.83
273 274 9.148104 ACGTGTATGGAAAAGTAGAGATAAAAC 57.852 33.333 0.00 0.00 0.00 2.43
278 279 5.125097 ACGACGTGTATGGAAAAGTAGAGAT 59.875 40.000 0.00 0.00 0.00 2.75
280 281 4.730657 ACGACGTGTATGGAAAAGTAGAG 58.269 43.478 0.00 0.00 0.00 2.43
283 284 5.369685 TGTACGACGTGTATGGAAAAGTA 57.630 39.130 11.56 0.00 35.02 2.24
284 285 4.241590 TGTACGACGTGTATGGAAAAGT 57.758 40.909 11.56 0.00 35.02 2.66
285 286 5.773239 AATGTACGACGTGTATGGAAAAG 57.227 39.130 11.56 0.00 35.02 2.27
308 315 8.420222 AGAAAATGGATTGTCATGTACACAAAA 58.580 29.630 0.00 0.00 38.00 2.44
364 371 5.284188 TGCAAAAGTTGAAAAACGTTAGTCG 59.716 36.000 0.00 0.00 46.00 4.18
463 472 7.487829 TCTTCCGTTTCTTCTTTCACATTTTTG 59.512 33.333 0.00 0.00 0.00 2.44
476 485 4.524749 CGTTTCCTTTCTTCCGTTTCTTC 58.475 43.478 0.00 0.00 0.00 2.87
479 488 2.289820 AGCGTTTCCTTTCTTCCGTTTC 59.710 45.455 0.00 0.00 0.00 2.78
486 495 1.609072 GCCTTCAGCGTTTCCTTTCTT 59.391 47.619 0.00 0.00 0.00 2.52
491 500 1.302832 CAGGCCTTCAGCGTTTCCT 60.303 57.895 0.00 0.00 45.17 3.36
492 501 1.600916 ACAGGCCTTCAGCGTTTCC 60.601 57.895 0.00 0.00 45.17 3.13
493 502 1.166531 ACACAGGCCTTCAGCGTTTC 61.167 55.000 0.00 0.00 45.17 2.78
497 506 2.743928 GGACACAGGCCTTCAGCG 60.744 66.667 0.00 0.00 45.17 5.18
570 581 5.452078 TGGGCTTTGATTAGTCTTTTGTG 57.548 39.130 0.00 0.00 0.00 3.33
573 584 4.022329 CCGTTGGGCTTTGATTAGTCTTTT 60.022 41.667 0.00 0.00 0.00 2.27
608 624 1.069668 AGGTCGGTTGTGAGTTACCAC 59.930 52.381 0.00 0.00 37.55 4.16
847 863 1.455959 CCCTGCCTACTACCTCGCT 60.456 63.158 0.00 0.00 0.00 4.93
866 882 3.727258 TGGGAAGGGATGGCGGTG 61.727 66.667 0.00 0.00 0.00 4.94
867 883 3.728373 GTGGGAAGGGATGGCGGT 61.728 66.667 0.00 0.00 0.00 5.68
887 903 1.069500 CAAACAAGGCGAGGTAAACGG 60.069 52.381 0.00 0.00 0.00 4.44
954 971 4.865365 TCGGTCACCAAATCAAAACAAAAC 59.135 37.500 0.00 0.00 0.00 2.43
955 972 5.073311 TCGGTCACCAAATCAAAACAAAA 57.927 34.783 0.00 0.00 0.00 2.44
956 973 4.440802 CCTCGGTCACCAAATCAAAACAAA 60.441 41.667 0.00 0.00 0.00 2.83
957 974 3.067461 CCTCGGTCACCAAATCAAAACAA 59.933 43.478 0.00 0.00 0.00 2.83
958 975 2.621055 CCTCGGTCACCAAATCAAAACA 59.379 45.455 0.00 0.00 0.00 2.83
971 988 1.451567 CTCTACGCCTCCTCGGTCA 60.452 63.158 0.00 0.00 34.25 4.02
974 991 3.955101 CGCTCTACGCCTCCTCGG 61.955 72.222 0.00 0.00 34.21 4.63
1014 1046 4.115199 AAGCGGTCCATGCCCTCC 62.115 66.667 0.00 0.00 0.00 4.30
1015 1047 1.686325 TAGAAGCGGTCCATGCCCTC 61.686 60.000 0.00 0.00 0.00 4.30
1016 1048 1.689233 TAGAAGCGGTCCATGCCCT 60.689 57.895 0.00 0.00 0.00 5.19
1017 1049 1.523938 GTAGAAGCGGTCCATGCCC 60.524 63.158 0.00 0.00 0.00 5.36
1019 1051 1.854227 GTAGTAGAAGCGGTCCATGC 58.146 55.000 0.00 0.00 0.00 4.06
1027 1059 1.359475 GGCCCTCGTAGTAGAAGCG 59.641 63.158 0.00 0.00 0.00 4.68
1115 1189 1.153489 TCCTCGGAGTCGTAGTCGG 60.153 63.158 4.02 0.00 37.69 4.79
1119 1193 1.750572 CGTCGTCCTCGGAGTCGTAG 61.751 65.000 15.52 9.60 37.69 3.51
1296 1391 4.393778 TCCTCCGTGTCCTCCCCC 62.394 72.222 0.00 0.00 0.00 5.40
1298 1414 1.075896 ATCTCCTCCGTGTCCTCCC 60.076 63.158 0.00 0.00 0.00 4.30
1306 1422 0.183971 AGGTCGATGATCTCCTCCGT 59.816 55.000 0.00 0.00 0.00 4.69
1307 1423 0.595588 CAGGTCGATGATCTCCTCCG 59.404 60.000 3.67 0.00 0.00 4.63
1315 1431 2.501128 CGTGGGCAGGTCGATGAT 59.499 61.111 0.00 0.00 0.00 2.45
1425 1541 1.838846 ATCATCCACCTCGGCCGAT 60.839 57.895 31.19 12.87 33.14 4.18
1505 1624 4.223953 TCCTCTCTTGTACCCCATCATAC 58.776 47.826 0.00 0.00 0.00 2.39
1609 1728 1.763545 GGCCTCCTTAAACTCCTCGAT 59.236 52.381 0.00 0.00 0.00 3.59
1718 1837 3.768757 CAGGACCTGATCTCTCTTCAAGT 59.231 47.826 17.22 0.00 32.44 3.16
1883 2351 0.249155 CATTGGCACATCATTCGCCC 60.249 55.000 0.00 0.00 45.63 6.13
1993 2461 1.977009 GCACCAAACTAGCCACCCC 60.977 63.158 0.00 0.00 0.00 4.95
2104 2572 2.422597 CAAACCAGCTGTATCGTCCAA 58.577 47.619 13.81 0.00 0.00 3.53
2219 2687 5.240183 CGGATCAGTAATGGATGAGCAAATT 59.760 40.000 0.00 0.00 33.55 1.82
2301 2769 1.820519 TGCAGCAAATCCTTCCATGAC 59.179 47.619 0.00 0.00 0.00 3.06
2375 2843 0.320771 CACCTCGCTAACCAGCTGTT 60.321 55.000 13.81 9.63 46.26 3.16
2632 3103 6.518208 AATAGAGTCACACAAGGTCTCTAC 57.482 41.667 0.00 0.00 39.47 2.59
2647 3118 5.642686 ACTCAGCTTGTAACGAATAGAGTC 58.357 41.667 0.00 0.00 0.00 3.36
2658 3129 3.510360 GGAGGACACTACTCAGCTTGTAA 59.490 47.826 0.00 0.00 36.70 2.41
3051 3522 1.279271 AGACCAGCCGTTAGAAGCATT 59.721 47.619 0.00 0.00 0.00 3.56
3119 3590 1.428912 AGCCCAAATTCTCCCTTGTCA 59.571 47.619 0.00 0.00 0.00 3.58
3121 3592 2.649816 AGTAGCCCAAATTCTCCCTTGT 59.350 45.455 0.00 0.00 0.00 3.16
3133 3604 1.419762 TGTTGCTCTCAAGTAGCCCAA 59.580 47.619 0.00 0.00 39.30 4.12
3189 3660 4.081087 ACTGAACGATAAGCTGGGTATTGT 60.081 41.667 0.00 0.00 0.00 2.71
3340 3811 6.773200 ACAGAATCTATGAAGATACTCACGGA 59.227 38.462 0.00 0.00 41.81 4.69
3360 3831 4.438880 GCATAGAGTAGTCGCTTGACAGAA 60.439 45.833 0.00 0.00 45.40 3.02
3403 3874 6.865834 AAGAGACACAGAACTCCATCTATT 57.134 37.500 0.00 0.00 34.13 1.73
3509 3980 1.272490 TGAAGACTTCTACACAGCGGG 59.728 52.381 16.02 0.00 0.00 6.13
3512 3983 5.119898 CACATTCTGAAGACTTCTACACAGC 59.880 44.000 16.02 0.00 0.00 4.40
3513 3984 5.636965 CCACATTCTGAAGACTTCTACACAG 59.363 44.000 16.02 5.73 0.00 3.66
3514 3985 5.541845 CCACATTCTGAAGACTTCTACACA 58.458 41.667 16.02 0.00 0.00 3.72
3515 3986 4.390297 GCCACATTCTGAAGACTTCTACAC 59.610 45.833 16.02 0.00 0.00 2.90
3741 4222 3.960102 AGGAAACACAGCAGGAAATGAAA 59.040 39.130 0.00 0.00 0.00 2.69
3750 4231 4.201753 CGATTATGTCAGGAAACACAGCAG 60.202 45.833 0.00 0.00 30.55 4.24
3787 4270 6.163135 AGTTAGATGCACACTAATAGTCCC 57.837 41.667 15.14 5.11 33.41 4.46
3824 4307 5.313712 GGAGGTTCCTGAATCTTTAACACA 58.686 41.667 0.00 0.00 30.64 3.72
3843 4326 4.263435 GAGGGAGTAGTACATATCGGAGG 58.737 52.174 2.52 0.00 0.00 4.30
3866 4349 7.228108 TGTTTACAGAGGGAGTAGTACATATCG 59.772 40.741 2.52 0.00 0.00 2.92
3868 4351 8.834004 TTGTTTACAGAGGGAGTAGTACATAT 57.166 34.615 2.52 0.00 0.00 1.78
3869 4352 8.654485 TTTGTTTACAGAGGGAGTAGTACATA 57.346 34.615 2.52 0.00 0.00 2.29
3871 4354 6.982160 TTTGTTTACAGAGGGAGTAGTACA 57.018 37.500 2.52 0.00 0.00 2.90
3872 4355 7.384477 ACATTTGTTTACAGAGGGAGTAGTAC 58.616 38.462 0.00 0.00 0.00 2.73
3873 4356 7.549147 ACATTTGTTTACAGAGGGAGTAGTA 57.451 36.000 0.00 0.00 0.00 1.82
3875 4358 8.095169 ACTTACATTTGTTTACAGAGGGAGTAG 58.905 37.037 0.00 0.00 0.00 2.57
3876 4359 7.876068 CACTTACATTTGTTTACAGAGGGAGTA 59.124 37.037 0.00 0.00 0.00 2.59
3878 4361 6.934645 TCACTTACATTTGTTTACAGAGGGAG 59.065 38.462 0.00 0.00 0.00 4.30
3879 4362 6.708949 GTCACTTACATTTGTTTACAGAGGGA 59.291 38.462 0.00 0.00 0.00 4.20
3880 4363 6.072673 GGTCACTTACATTTGTTTACAGAGGG 60.073 42.308 0.00 0.00 0.00 4.30
3881 4364 6.710744 AGGTCACTTACATTTGTTTACAGAGG 59.289 38.462 0.00 0.00 0.00 3.69
3882 4365 7.730364 AGGTCACTTACATTTGTTTACAGAG 57.270 36.000 0.00 0.00 0.00 3.35
3883 4366 9.616156 TTTAGGTCACTTACATTTGTTTACAGA 57.384 29.630 0.00 0.00 0.00 3.41
3886 4369 9.161684 CGTTTTAGGTCACTTACATTTGTTTAC 57.838 33.333 0.00 0.00 0.00 2.01
3887 4370 8.891720 ACGTTTTAGGTCACTTACATTTGTTTA 58.108 29.630 0.00 0.00 0.00 2.01
3888 4371 7.764331 ACGTTTTAGGTCACTTACATTTGTTT 58.236 30.769 0.00 0.00 0.00 2.83
3889 4372 7.281549 AGACGTTTTAGGTCACTTACATTTGTT 59.718 33.333 0.00 0.00 35.60 2.83
3890 4373 6.764560 AGACGTTTTAGGTCACTTACATTTGT 59.235 34.615 0.00 0.00 35.60 2.83
3891 4374 7.186021 AGACGTTTTAGGTCACTTACATTTG 57.814 36.000 0.00 0.00 35.60 2.32
3892 4375 7.797038 AAGACGTTTTAGGTCACTTACATTT 57.203 32.000 0.00 0.00 35.60 2.32
3893 4376 7.927629 TGTAAGACGTTTTAGGTCACTTACATT 59.072 33.333 13.51 0.00 33.12 2.71
3894 4377 7.436118 TGTAAGACGTTTTAGGTCACTTACAT 58.564 34.615 13.51 0.00 33.12 2.29
3895 4378 6.804677 TGTAAGACGTTTTAGGTCACTTACA 58.195 36.000 13.51 13.51 34.37 2.41
3896 4379 7.880059 ATGTAAGACGTTTTAGGTCACTTAC 57.120 36.000 0.00 0.00 35.60 2.34
3897 4380 8.767085 CAAATGTAAGACGTTTTAGGTCACTTA 58.233 33.333 0.00 0.00 35.31 2.24
3898 4381 7.281549 ACAAATGTAAGACGTTTTAGGTCACTT 59.718 33.333 0.00 0.00 35.31 3.16
3933 4416 7.329471 GCAAAAACTTTCATCCATCTAAACTCC 59.671 37.037 0.00 0.00 0.00 3.85
3934 4417 8.084684 AGCAAAAACTTTCATCCATCTAAACTC 58.915 33.333 0.00 0.00 0.00 3.01
3935 4418 7.869429 CAGCAAAAACTTTCATCCATCTAAACT 59.131 33.333 0.00 0.00 0.00 2.66
3936 4419 7.653311 ACAGCAAAAACTTTCATCCATCTAAAC 59.347 33.333 0.00 0.00 0.00 2.01
4053 4734 0.036306 CAAACAGTCCGGGTAAGCCT 59.964 55.000 0.00 0.00 34.45 4.58
4194 4876 3.319122 ACTGAAAGCAGGGATTGACAAAC 59.681 43.478 0.00 0.00 46.60 2.93
4234 4916 9.646522 ACTGCAGTTCCAAAAATATATATCCTT 57.353 29.630 15.25 0.00 0.00 3.36
4235 4917 9.646522 AACTGCAGTTCCAAAAATATATATCCT 57.353 29.630 26.36 0.00 31.64 3.24
4236 4918 9.899226 GAACTGCAGTTCCAAAAATATATATCC 57.101 33.333 38.44 15.74 46.42 2.59
4362 5044 6.491062 CAGCAGATTATTGGGGATGATTGTAA 59.509 38.462 0.00 0.00 0.00 2.41
4374 5056 9.764870 CGATAAAATACATCAGCAGATTATTGG 57.235 33.333 0.00 0.00 30.20 3.16
4415 5097 7.230849 TGAAATGCCAATAACTCAAACTGAT 57.769 32.000 0.00 0.00 0.00 2.90
4425 5107 3.096092 TCCACCCTGAAATGCCAATAAC 58.904 45.455 0.00 0.00 0.00 1.89
4441 5123 4.340950 TGAAAGACCTGTGAAATTTCCACC 59.659 41.667 15.48 4.46 33.80 4.61


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

AutoCloner maintained by Alex Coulton.