Multiple sequence alignment - TraesCS1A01G250900

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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 TraesCS1A01G250900 chr1A 100.000 4693 0 0 1 4693 442564284 442559592 0.000000e+00 8667.0
1 TraesCS1A01G250900 chr1D 90.181 1935 100 31 2171 4033 342863043 342861127 0.000000e+00 2438.0
2 TraesCS1A01G250900 chr1D 89.854 1784 97 41 426 2170 342864741 342863003 0.000000e+00 2215.0
3 TraesCS1A01G250900 chr1D 93.944 611 30 5 4082 4689 342861129 342860523 0.000000e+00 917.0
4 TraesCS1A01G250900 chr1D 94.923 453 21 1 16 466 342865295 342864843 0.000000e+00 708.0
5 TraesCS1A01G250900 chr1B 90.484 1839 94 34 374 2171 459929339 459927541 0.000000e+00 2351.0
6 TraesCS1A01G250900 chr1B 91.459 1124 48 12 2952 4033 459926623 459925506 0.000000e+00 1500.0
7 TraesCS1A01G250900 chr1B 93.445 595 28 5 4102 4689 459925501 459924911 0.000000e+00 872.0
8 TraesCS1A01G250900 chr1B 86.765 816 63 23 2170 2956 459927583 459926784 0.000000e+00 867.0
9 TraesCS1A01G250900 chr1B 95.359 474 21 1 1 473 459930036 459929563 0.000000e+00 752.0
10 TraesCS1A01G250900 chr5B 82.828 693 78 27 35 708 686754851 686755521 2.430000e-162 582.0
11 TraesCS1A01G250900 chr5B 94.340 53 3 0 4032 4084 574906689 574906741 1.080000e-11 82.4
12 TraesCS1A01G250900 chr7B 81.412 694 71 37 35 708 486727238 486726583 9.000000e-142 514.0
13 TraesCS1A01G250900 chr7B 84.182 373 39 11 35 407 60370526 60370878 1.250000e-90 344.0
14 TraesCS1A01G250900 chr7B 87.500 56 4 1 4032 4084 552029519 552029574 1.410000e-05 62.1
15 TraesCS1A01G250900 chr2B 83.216 566 57 18 35 581 798306079 798305533 7.060000e-133 484.0
16 TraesCS1A01G250900 chr2B 91.489 47 4 0 4050 4096 518048359 518048313 1.090000e-06 65.8
17 TraesCS1A01G250900 chr4B 84.987 373 39 10 35 407 59869750 59869395 3.450000e-96 363.0
18 TraesCS1A01G250900 chrUn 85.600 250 33 3 158 407 395472875 395473121 4.660000e-65 259.0
19 TraesCS1A01G250900 chr5D 91.803 61 2 2 4031 4089 459929295 459929354 1.080000e-11 82.4
20 TraesCS1A01G250900 chr5D 86.207 58 5 2 4027 4084 244705843 244705789 5.070000e-05 60.2
21 TraesCS1A01G250900 chr6B 93.023 43 1 2 4055 4096 354218725 354218766 1.410000e-05 62.1
22 TraesCS1A01G250900 chr6B 91.304 46 0 3 4055 4098 21137167 21137124 5.070000e-05 60.2
23 TraesCS1A01G250900 chr4D 91.111 45 2 2 4050 4092 57077909 57077865 5.070000e-05 60.2
24 TraesCS1A01G250900 chr3B 92.857 42 1 2 4050 4089 47462139 47462098 5.070000e-05 60.2


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 TraesCS1A01G250900 chr1A 442559592 442564284 4692 True 8667.0 8667 100.0000 1 4693 1 chr1A.!!$R1 4692
1 TraesCS1A01G250900 chr1D 342860523 342865295 4772 True 1569.5 2438 92.2255 16 4689 4 chr1D.!!$R1 4673
2 TraesCS1A01G250900 chr1B 459924911 459930036 5125 True 1268.4 2351 91.5024 1 4689 5 chr1B.!!$R1 4688
3 TraesCS1A01G250900 chr5B 686754851 686755521 670 False 582.0 582 82.8280 35 708 1 chr5B.!!$F2 673
4 TraesCS1A01G250900 chr7B 486726583 486727238 655 True 514.0 514 81.4120 35 708 1 chr7B.!!$R1 673
5 TraesCS1A01G250900 chr2B 798305533 798306079 546 True 484.0 484 83.2160 35 581 1 chr2B.!!$R2 546

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
415 418 0.668401 AAACGGTTAGCGTTCCCTCG 60.668 55.0 22.06 0.0 0.0 4.63 F
1483 1840 0.667487 TCACTCGCCTTCTTCGCAAG 60.667 55.0 0.00 0.0 0.0 4.01 F
2397 2787 0.032130 GTGAGTGAGGTGAGCAACGA 59.968 55.0 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 2310 0.108329 AGCCGTATTGGTGAAGTCCG 60.108 55.000 0.0 0.0 41.21 4.79 R
2476 2870 2.388735 TCATGACCTACCAGTAGCCAG 58.611 52.381 0.0 0.0 31.95 4.85 R
4055 4684 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.0 0.0 0.00 4.46 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
33 34 2.556144 TCTCACCAGGATATGCATGC 57.444 50.000 11.82 11.82 0.00 4.06
159 160 5.760253 TGGAGACTTGTCTGATTCAAAGTTC 59.240 40.000 8.11 4.57 0.00 3.01
171 172 1.013596 CAAAGTTCGTCACCAGTGCA 58.986 50.000 0.00 0.00 0.00 4.57
281 284 2.642427 ACGATGATGTTAATGCCAGCA 58.358 42.857 0.00 0.00 32.10 4.41
305 308 3.253188 TGCCTAAACTTTGATGACTGCAC 59.747 43.478 0.00 0.00 0.00 4.57
334 337 7.507277 AGATGGTCTAGCTGTACAGATAAATGA 59.493 37.037 27.08 14.81 0.00 2.57
411 414 1.193874 CAGTGAAACGGTTAGCGTTCC 59.806 52.381 22.06 11.02 45.86 3.62
415 418 0.668401 AAACGGTTAGCGTTCCCTCG 60.668 55.000 22.06 0.00 0.00 4.63
421 424 2.745821 GGTTAGCGTTCCCTCGAAAATT 59.254 45.455 0.00 0.00 0.00 1.82
471 796 1.047801 TGCAGAGCACCTTAGTCACA 58.952 50.000 0.00 0.00 31.71 3.58
473 798 1.270305 GCAGAGCACCTTAGTCACACA 60.270 52.381 0.00 0.00 0.00 3.72
600 932 1.826385 GGCCAATCTCATATTCCCGG 58.174 55.000 0.00 0.00 0.00 5.73
864 1215 2.770164 AAGGATCAGAGACCAAACCG 57.230 50.000 0.00 0.00 0.00 4.44
923 1274 1.450312 CCCATTGGACGGCTGAGAC 60.450 63.158 3.62 0.00 0.00 3.36
950 1301 2.577059 GTCAGATCGACGGCCCAA 59.423 61.111 0.00 0.00 34.19 4.12
955 1306 4.388499 ATCGACGGCCCAAAGCGT 62.388 61.111 0.00 0.00 45.17 5.07
1014 1365 1.731720 GAGGCATCCATCGATTAGCC 58.268 55.000 15.62 15.62 37.68 3.93
1015 1366 1.002430 GAGGCATCCATCGATTAGCCA 59.998 52.381 21.94 0.00 39.15 4.75
1016 1367 1.002888 AGGCATCCATCGATTAGCCAG 59.997 52.381 21.94 1.44 39.15 4.85
1224 1581 2.643232 GCAGGTAGGGTTCCGTCGT 61.643 63.158 0.00 0.00 0.00 4.34
1225 1582 1.969862 CAGGTAGGGTTCCGTCGTT 59.030 57.895 0.00 0.00 0.00 3.85
1479 1836 2.094417 GGATTTTCACTCGCCTTCTTCG 59.906 50.000 0.00 0.00 0.00 3.79
1483 1840 0.667487 TCACTCGCCTTCTTCGCAAG 60.667 55.000 0.00 0.00 0.00 4.01
1486 1843 2.174349 CGCCTTCTTCGCAAGTGC 59.826 61.111 0.00 0.00 39.48 4.40
1506 1863 1.673337 TCATGTGCTCAGTGCCTGC 60.673 57.895 0.00 0.00 42.00 4.85
1533 1899 3.818773 CCGGTTTACTGACTGGATTGTTT 59.181 43.478 0.00 0.00 46.98 2.83
1566 1932 1.078143 GCAGATGGGGTTCTTCGCT 60.078 57.895 0.00 0.00 0.00 4.93
1704 2070 2.928801 TGGTTCAGTGCAAGCTCTTA 57.071 45.000 0.00 0.00 0.00 2.10
1749 2116 2.223971 ACTCGAATTGTGTCGGTTCACT 60.224 45.455 0.00 0.00 41.43 3.41
1844 2211 2.158682 TGGTGATGTGCCAAACTACACT 60.159 45.455 0.00 0.00 37.68 3.55
1850 2217 3.386486 TGTGCCAAACTACACTACTTCG 58.614 45.455 0.00 0.00 37.68 3.79
1876 2243 2.760634 TCGGTATGCTTCTTTCTGCA 57.239 45.000 0.00 0.00 43.67 4.41
1891 2258 9.383519 CTTCTTTCTGCATATAAGTGGTTCTTA 57.616 33.333 0.00 0.00 41.98 2.10
1894 2261 8.492673 TTTCTGCATATAAGTGGTTCTTACTG 57.507 34.615 0.00 0.00 40.80 2.74
1897 2264 7.764443 TCTGCATATAAGTGGTTCTTACTGTTC 59.236 37.037 0.00 0.00 40.80 3.18
1921 2298 7.177184 TCTTTTTATCTTTGGTAACTACCCCC 58.823 38.462 3.45 0.00 45.87 5.40
1932 2309 0.611714 ACTACCCCCGCTTGTTACTG 59.388 55.000 0.00 0.00 0.00 2.74
1933 2310 0.743345 CTACCCCCGCTTGTTACTGC 60.743 60.000 0.00 0.00 0.00 4.40
1949 2326 0.999406 CTGCGGACTTCACCAATACG 59.001 55.000 0.00 0.00 0.00 3.06
1951 2328 1.702491 GCGGACTTCACCAATACGGC 61.702 60.000 0.00 0.00 39.03 5.68
1954 2331 2.007608 GGACTTCACCAATACGGCTTC 58.992 52.381 0.00 0.00 39.03 3.86
1955 2332 2.614481 GGACTTCACCAATACGGCTTCA 60.614 50.000 0.00 0.00 39.03 3.02
1956 2333 3.270877 GACTTCACCAATACGGCTTCAT 58.729 45.455 0.00 0.00 39.03 2.57
1957 2334 3.009723 ACTTCACCAATACGGCTTCATG 58.990 45.455 0.00 0.00 39.03 3.07
1959 2336 2.627945 TCACCAATACGGCTTCATGTC 58.372 47.619 0.00 0.00 39.03 3.06
1960 2337 2.027653 TCACCAATACGGCTTCATGTCA 60.028 45.455 0.00 0.00 39.03 3.58
1961 2338 2.945008 CACCAATACGGCTTCATGTCAT 59.055 45.455 0.00 0.00 39.03 3.06
1962 2339 2.945008 ACCAATACGGCTTCATGTCATG 59.055 45.455 6.47 6.47 39.03 3.07
1963 2340 2.945008 CCAATACGGCTTCATGTCATGT 59.055 45.455 12.54 0.00 0.00 3.21
1965 2342 4.574421 CCAATACGGCTTCATGTCATGTAA 59.426 41.667 12.54 5.37 0.00 2.41
1966 2343 5.065859 CCAATACGGCTTCATGTCATGTAAA 59.934 40.000 12.54 0.15 0.00 2.01
1968 2345 6.751514 ATACGGCTTCATGTCATGTAAAAA 57.248 33.333 12.54 0.00 0.00 1.94
1969 2346 5.643379 ACGGCTTCATGTCATGTAAAAAT 57.357 34.783 12.54 0.00 0.00 1.82
2013 2403 6.951643 ACTTAGGCTTAAAACACGTTACTTG 58.048 36.000 0.00 0.00 0.00 3.16
2034 2424 7.290813 ACTTGGACTAATCTCTTTTGACCTTT 58.709 34.615 0.00 0.00 0.00 3.11
2079 2469 8.257306 TCAAATTTACACTGCTTTTCCTTTCTT 58.743 29.630 0.00 0.00 0.00 2.52
2126 2516 5.241728 AGTTTCATAAGAGGTTGTTTGGCTC 59.758 40.000 0.00 0.00 0.00 4.70
2145 2535 6.378582 TGGCTCGTTGAGAAATTAAATCAAC 58.621 36.000 15.32 15.32 45.92 3.18
2167 2557 5.245531 ACGAGATACCACATGTCACAATTT 58.754 37.500 0.00 0.00 0.00 1.82
2168 2558 6.403049 ACGAGATACCACATGTCACAATTTA 58.597 36.000 0.00 0.00 0.00 1.40
2169 2559 7.047891 ACGAGATACCACATGTCACAATTTAT 58.952 34.615 0.00 0.00 0.00 1.40
2170 2560 7.552687 ACGAGATACCACATGTCACAATTTATT 59.447 33.333 0.00 0.00 0.00 1.40
2171 2561 7.852454 CGAGATACCACATGTCACAATTTATTG 59.148 37.037 0.00 1.03 43.26 1.90
2172 2562 8.806429 AGATACCACATGTCACAATTTATTGA 57.194 30.769 9.32 0.00 40.14 2.57
2173 2563 8.896744 AGATACCACATGTCACAATTTATTGAG 58.103 33.333 9.32 1.85 40.14 3.02
2174 2564 8.806429 ATACCACATGTCACAATTTATTGAGA 57.194 30.769 9.32 4.20 40.14 3.27
2175 2565 7.523293 ACCACATGTCACAATTTATTGAGAA 57.477 32.000 9.32 0.14 38.69 2.87
2176 2566 7.950512 ACCACATGTCACAATTTATTGAGAAA 58.049 30.769 9.32 2.76 38.69 2.52
2177 2567 8.587608 ACCACATGTCACAATTTATTGAGAAAT 58.412 29.630 9.32 4.89 38.69 2.17
2178 2568 9.426837 CCACATGTCACAATTTATTGAGAAATT 57.573 29.630 9.32 0.00 38.69 1.82
2196 2586 9.904198 TGAGAAATTAAATCATGAGATACCACA 57.096 29.630 0.09 0.00 33.08 4.17
2201 2591 9.631257 AATTAAATCATGAGATACCACATGTCA 57.369 29.630 0.09 0.00 42.75 3.58
2202 2592 6.932356 AAATCATGAGATACCACATGTCAC 57.068 37.500 0.09 0.00 42.75 3.67
2203 2593 5.619132 ATCATGAGATACCACATGTCACA 57.381 39.130 0.09 0.00 42.75 3.58
2204 2594 5.419239 TCATGAGATACCACATGTCACAA 57.581 39.130 0.00 0.00 42.75 3.33
2205 2595 5.993055 TCATGAGATACCACATGTCACAAT 58.007 37.500 0.00 0.00 42.75 2.71
2206 2596 6.417258 TCATGAGATACCACATGTCACAATT 58.583 36.000 0.00 0.00 42.75 2.32
2207 2597 7.563906 TCATGAGATACCACATGTCACAATTA 58.436 34.615 0.00 0.00 42.75 1.40
2208 2598 8.046107 TCATGAGATACCACATGTCACAATTAA 58.954 33.333 0.00 0.00 42.75 1.40
2209 2599 8.843262 CATGAGATACCACATGTCACAATTAAT 58.157 33.333 0.00 0.00 38.98 1.40
2289 2679 1.824230 AGTTGCACAAAAGGTTGCTCA 59.176 42.857 0.00 0.00 38.39 4.26
2330 2720 8.561738 AAAGAAAAGAGACAAAGTACACAAGA 57.438 30.769 0.00 0.00 0.00 3.02
2365 2755 4.717279 AAGAAGGTTTACAGGTAGGCAA 57.283 40.909 0.00 0.00 0.00 4.52
2397 2787 0.032130 GTGAGTGAGGTGAGCAACGA 59.968 55.000 0.00 0.00 0.00 3.85
2398 2788 0.315251 TGAGTGAGGTGAGCAACGAG 59.685 55.000 0.00 0.00 0.00 4.18
2429 2819 0.850100 TCCAACCACCATCACCAACT 59.150 50.000 0.00 0.00 0.00 3.16
2430 2820 1.202879 TCCAACCACCATCACCAACTC 60.203 52.381 0.00 0.00 0.00 3.01
2431 2821 1.247567 CAACCACCATCACCAACTCC 58.752 55.000 0.00 0.00 0.00 3.85
2432 2822 0.112412 AACCACCATCACCAACTCCC 59.888 55.000 0.00 0.00 0.00 4.30
2433 2823 0.772124 ACCACCATCACCAACTCCCT 60.772 55.000 0.00 0.00 0.00 4.20
2434 2824 0.405585 CCACCATCACCAACTCCCTT 59.594 55.000 0.00 0.00 0.00 3.95
2450 2840 8.977412 CCAACTCCCTTTTATGTTATGGTAAAT 58.023 33.333 0.00 0.00 0.00 1.40
2480 2874 9.982651 TGTGAAGATAATATAAAGACTACTGGC 57.017 33.333 0.00 0.00 0.00 4.85
2521 2915 6.465084 AGTATCCACTTGTTGGTTTACTCTC 58.535 40.000 0.00 0.00 46.97 3.20
2535 2929 5.880332 GGTTTACTCTCATTGTGGCATCTTA 59.120 40.000 0.00 0.00 0.00 2.10
2560 2956 8.891671 AGAAATGAAATTGTGTGCTTGTATTT 57.108 26.923 0.00 0.00 36.10 1.40
2588 2987 3.273434 CTGCATATAATGGTGGGATCCG 58.727 50.000 5.45 0.00 0.00 4.18
2596 3014 0.468226 TGGTGGGATCCGTATGCTTC 59.532 55.000 5.45 0.00 0.00 3.86
2597 3015 0.250338 GGTGGGATCCGTATGCTTCC 60.250 60.000 5.45 0.00 0.00 3.46
2673 3092 9.635404 ATGGGTATCGTTATGAAATTAAAAGGA 57.365 29.630 0.00 0.00 0.00 3.36
2698 3117 7.789273 ATTGTTCTGTTGAAAATGATTTGCA 57.211 28.000 0.00 0.00 33.52 4.08
2699 3118 7.606858 TTGTTCTGTTGAAAATGATTTGCAA 57.393 28.000 7.22 7.22 33.52 4.08
2701 3120 7.631822 TGTTCTGTTGAAAATGATTTGCAATG 58.368 30.769 14.00 10.38 33.52 2.82
2702 3121 6.788684 TCTGTTGAAAATGATTTGCAATGG 57.211 33.333 14.00 10.04 0.00 3.16
2762 3181 6.476706 GTCTGGTTCAGGTGAAAATTCAAAAG 59.523 38.462 0.00 0.00 39.21 2.27
2892 3311 3.831911 TCCTTTAGAATTTTGTGGCAGGG 59.168 43.478 0.00 0.00 0.00 4.45
3053 3637 8.712363 TCGCAAATAGCAATCTTGATATAACTC 58.288 33.333 1.47 0.00 46.13 3.01
3054 3638 8.498358 CGCAAATAGCAATCTTGATATAACTCA 58.502 33.333 1.47 0.00 46.13 3.41
3213 3797 8.547069 GTGCACTAATCTATGAGAAGATGTTTC 58.453 37.037 10.32 0.00 36.34 2.78
3214 3798 8.260114 TGCACTAATCTATGAGAAGATGTTTCA 58.740 33.333 0.00 0.00 36.34 2.69
3262 3846 4.553330 TTCTGTCTTCCTGGACCATAAC 57.447 45.455 0.00 0.00 35.54 1.89
3669 4259 7.883391 TCTTTTTAACTGTGGTGGTTGATAA 57.117 32.000 0.00 0.00 0.00 1.75
3686 4286 7.227910 TGGTTGATAAGTTTAGTTGTCTGAACC 59.772 37.037 0.00 0.00 39.84 3.62
3704 4304 0.393537 CCTCCAGACCAGATTGTGCC 60.394 60.000 0.00 0.00 0.00 5.01
3716 4316 1.205179 GATTGTGCCAACCATGCATCA 59.795 47.619 0.00 0.00 41.46 3.07
3723 4323 1.745087 CCAACCATGCATCACACCTAC 59.255 52.381 0.00 0.00 0.00 3.18
3749 4349 6.220201 TCACTTTGTCTCACATTTGACGATA 58.780 36.000 0.00 0.00 36.10 2.92
3826 4428 1.937278 ATGCTCTCAAGTGCGATGAG 58.063 50.000 6.83 6.83 44.53 2.90
3841 4457 5.748630 GTGCGATGAGAGTATTTGATACACA 59.251 40.000 0.00 0.00 38.21 3.72
3871 4488 2.943033 AGGTTCTTCCACTTTGACAACG 59.057 45.455 0.00 0.00 39.02 4.10
3872 4489 2.032924 GGTTCTTCCACTTTGACAACGG 59.967 50.000 0.00 0.00 35.97 4.44
4033 4662 9.931210 GCAATATGTAACCTACTTCAAATGTAC 57.069 33.333 0.00 0.00 0.00 2.90
4037 4666 6.704310 TGTAACCTACTTCAAATGTACTCCC 58.296 40.000 0.00 0.00 0.00 4.30
4038 4667 6.499350 TGTAACCTACTTCAAATGTACTCCCT 59.501 38.462 0.00 0.00 0.00 4.20
4039 4668 5.678955 ACCTACTTCAAATGTACTCCCTC 57.321 43.478 0.00 0.00 0.00 4.30
4040 4669 4.470304 ACCTACTTCAAATGTACTCCCTCC 59.530 45.833 0.00 0.00 0.00 4.30
4041 4670 4.469945 CCTACTTCAAATGTACTCCCTCCA 59.530 45.833 0.00 0.00 0.00 3.86
4042 4671 5.131142 CCTACTTCAAATGTACTCCCTCCAT 59.869 44.000 0.00 0.00 0.00 3.41
4043 4672 5.104259 ACTTCAAATGTACTCCCTCCATC 57.896 43.478 0.00 0.00 0.00 3.51
4044 4673 4.080299 ACTTCAAATGTACTCCCTCCATCC 60.080 45.833 0.00 0.00 0.00 3.51
4045 4674 3.459828 TCAAATGTACTCCCTCCATCCA 58.540 45.455 0.00 0.00 0.00 3.41
4046 4675 3.849574 TCAAATGTACTCCCTCCATCCAA 59.150 43.478 0.00 0.00 0.00 3.53
4047 4676 4.290985 TCAAATGTACTCCCTCCATCCAAA 59.709 41.667 0.00 0.00 0.00 3.28
4048 4677 4.946160 AATGTACTCCCTCCATCCAAAA 57.054 40.909 0.00 0.00 0.00 2.44
4049 4678 4.946160 ATGTACTCCCTCCATCCAAAAA 57.054 40.909 0.00 0.00 0.00 1.94
4070 4699 2.902065 GCTAGGGACAAGCTTTTTCG 57.098 50.000 0.00 0.00 37.01 3.46
4071 4700 1.468914 GCTAGGGACAAGCTTTTTCGG 59.531 52.381 0.00 0.00 37.01 4.30
4072 4701 2.874457 GCTAGGGACAAGCTTTTTCGGA 60.874 50.000 0.00 0.00 37.01 4.55
4073 4702 1.605753 AGGGACAAGCTTTTTCGGAC 58.394 50.000 0.00 0.00 0.00 4.79
4074 4703 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
4075 4704 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
4076 4705 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
4077 4706 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
4078 4707 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
4079 4708 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
4080 4709 1.004200 GCTTTTTCGGACGGAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
4081 4710 1.019805 GCTTTTTCGGACGGAGGGAG 61.020 60.000 0.00 0.00 0.00 4.30
4082 4711 0.320697 CTTTTTCGGACGGAGGGAGT 59.679 55.000 0.00 0.00 0.00 3.85
4083 4712 1.547372 CTTTTTCGGACGGAGGGAGTA 59.453 52.381 0.00 0.00 0.00 2.59
4095 4724 1.555075 GAGGGAGTAACACTGATGCCA 59.445 52.381 0.00 0.00 29.26 4.92
4145 4774 1.542547 CCTGCTTAGAACCCAACGTGT 60.543 52.381 0.00 0.00 0.00 4.49
4214 4843 7.431084 CACGCTGTACAAAGAAATTACAAACTT 59.569 33.333 0.00 0.00 0.00 2.66
4236 4865 2.283101 TTGGCCACTGTCCATGCC 60.283 61.111 3.88 0.00 44.27 4.40
4273 4902 3.197790 CCGAATGTGCTGCTCCCG 61.198 66.667 0.00 1.62 0.00 5.14
4291 4920 2.094752 CCCGTGATGTCCCAAAATTGAC 60.095 50.000 0.00 0.00 0.00 3.18
4293 4922 3.119849 CCGTGATGTCCCAAAATTGACTC 60.120 47.826 0.00 0.00 32.67 3.36
4297 4926 4.520111 TGATGTCCCAAAATTGACTCTGTG 59.480 41.667 0.00 0.00 32.67 3.66
4384 5016 9.349713 TGAAACCATCAAGATGTTAGTAAGTTT 57.650 29.630 9.04 9.31 37.11 2.66
4386 5018 8.918202 AACCATCAAGATGTTAGTAAGTTTGA 57.082 30.769 9.04 0.00 37.11 2.69
4412 5048 9.567776 AATGAACCACCACGATTATGAAATATA 57.432 29.630 0.00 0.00 0.00 0.86
4414 5050 9.567776 TGAACCACCACGATTATGAAATATAAT 57.432 29.630 0.00 0.00 0.00 1.28
4626 5262 9.092876 CAGAAAGAATCAGAGGTAATCAAGTAC 57.907 37.037 0.00 0.00 0.00 2.73
4627 5263 9.041354 AGAAAGAATCAGAGGTAATCAAGTACT 57.959 33.333 0.00 0.00 0.00 2.73
4689 5325 9.046846 TGGGTTCCATATAAGTAGATTCCATAG 57.953 37.037 0.00 0.00 0.00 2.23
4690 5326 9.047947 GGGTTCCATATAAGTAGATTCCATAGT 57.952 37.037 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.854963 TGCATATCCTGGTGAGAATGC 58.145 47.619 11.61 11.61 42.47 3.56
33 34 3.060615 GCTGCCCTGGAAGCACTG 61.061 66.667 11.49 0.00 45.89 3.66
159 160 3.349006 GGCACTGCACTGGTGACG 61.349 66.667 8.64 0.00 36.89 4.35
281 284 3.503748 GCAGTCATCAAAGTTTAGGCACT 59.496 43.478 0.00 0.00 46.37 4.40
305 308 4.203226 TCTGTACAGCTAGACCATCTCTG 58.797 47.826 18.45 0.00 0.00 3.35
411 414 6.671402 GCAAATTGATGCTCAAATTTTCGAGG 60.671 38.462 0.00 0.00 40.12 4.63
415 418 8.018520 TGATTGCAAATTGATGCTCAAATTTTC 58.981 29.630 1.71 0.00 46.54 2.29
421 424 7.597369 GCTATATGATTGCAAATTGATGCTCAA 59.403 33.333 1.71 1.85 46.54 3.02
468 793 3.127589 TCCGTTGTTGTATCAGTGTGTG 58.872 45.455 0.00 0.00 0.00 3.82
471 796 2.224185 TGCTCCGTTGTTGTATCAGTGT 60.224 45.455 0.00 0.00 0.00 3.55
473 798 2.831685 TGCTCCGTTGTTGTATCAGT 57.168 45.000 0.00 0.00 0.00 3.41
600 932 1.081242 CAATGTTGCGGTGTCTGGC 60.081 57.895 0.00 0.00 0.00 4.85
801 1150 1.350019 CCTGACGGAAAAACCCTACCT 59.650 52.381 0.00 0.00 34.64 3.08
842 1191 3.821033 CGGTTTGGTCTCTGATCCTTTTT 59.179 43.478 0.00 0.00 0.00 1.94
849 1198 1.827969 CTCCTCGGTTTGGTCTCTGAT 59.172 52.381 0.00 0.00 0.00 2.90
864 1215 1.063867 TCACCCCTACTAGTGCTCCTC 60.064 57.143 5.39 0.00 33.90 3.71
918 1269 3.749064 GACCTCCAGCGCGTCTCA 61.749 66.667 8.43 0.00 0.00 3.27
923 1274 2.279120 GATCTGACCTCCAGCGCG 60.279 66.667 0.00 0.00 42.62 6.86
960 1311 1.353091 GGGGAGTAATAGCCCTGAGG 58.647 60.000 0.00 0.00 44.10 3.86
1064 1421 4.816984 TCCTCCTCCTCGTCGGCC 62.817 72.222 0.00 0.00 0.00 6.13
1065 1422 3.213402 CTCCTCCTCCTCGTCGGC 61.213 72.222 0.00 0.00 0.00 5.54
1066 1423 2.517402 CCTCCTCCTCCTCGTCGG 60.517 72.222 0.00 0.00 0.00 4.79
1067 1424 1.525077 CTCCTCCTCCTCCTCGTCG 60.525 68.421 0.00 0.00 0.00 5.12
1068 1425 0.179029 CTCTCCTCCTCCTCCTCGTC 60.179 65.000 0.00 0.00 0.00 4.20
1069 1426 1.641552 CCTCTCCTCCTCCTCCTCGT 61.642 65.000 0.00 0.00 0.00 4.18
1073 1430 2.123033 GGCCTCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
1479 1836 1.154338 GAGCACATGACGCACTTGC 60.154 57.895 13.07 4.62 37.78 4.01
1483 1840 1.494628 CACTGAGCACATGACGCAC 59.505 57.895 13.07 8.12 0.00 5.34
1506 1863 1.005394 AGTCAGTAAACCGGGCACG 60.005 57.895 6.32 0.00 40.55 5.34
1533 1899 4.264253 CCATCTGCAGAACCAACAAGATA 58.736 43.478 22.50 0.00 0.00 1.98
1686 2052 2.494059 TGTAAGAGCTTGCACTGAACC 58.506 47.619 0.00 0.00 30.38 3.62
1704 2070 1.541147 CGGCACAACCAAATCAGATGT 59.459 47.619 0.00 0.00 39.03 3.06
1749 2116 8.651588 CAACACACAAGCACACTTAATTTTTAA 58.348 29.630 0.00 0.00 33.74 1.52
1844 2211 2.230508 GCATACCGATCCATCCGAAGTA 59.769 50.000 0.00 0.00 0.00 2.24
1850 2217 3.409026 AAGAAGCATACCGATCCATCC 57.591 47.619 0.00 0.00 0.00 3.51
1932 2309 1.702491 GCCGTATTGGTGAAGTCCGC 61.702 60.000 0.00 0.00 41.21 5.54
1933 2310 0.108329 AGCCGTATTGGTGAAGTCCG 60.108 55.000 0.00 0.00 41.21 4.79
1974 2356 5.816682 AGCCTAAGTTGTATTGGTAAAGCT 58.183 37.500 0.00 0.00 0.00 3.74
1975 2357 6.510879 AAGCCTAAGTTGTATTGGTAAAGC 57.489 37.500 0.00 0.00 0.00 3.51
1979 2361 8.785946 GTGTTTTAAGCCTAAGTTGTATTGGTA 58.214 33.333 0.00 0.00 0.00 3.25
2050 2440 9.476202 AAAGGAAAAGCAGTGTAAATTTGATAC 57.524 29.630 0.00 0.00 0.00 2.24
2052 2442 8.424133 AGAAAGGAAAAGCAGTGTAAATTTGAT 58.576 29.630 0.00 0.00 0.00 2.57
2106 2496 3.244422 ACGAGCCAAACAACCTCTTATGA 60.244 43.478 0.00 0.00 0.00 2.15
2118 2508 6.861055 TGATTTAATTTCTCAACGAGCCAAAC 59.139 34.615 0.00 0.00 0.00 2.93
2145 2535 5.801350 AAATTGTGACATGTGGTATCTCG 57.199 39.130 1.15 0.00 0.00 4.04
2170 2560 9.904198 TGTGGTATCTCATGATTTAATTTCTCA 57.096 29.630 0.00 0.00 34.32 3.27
2175 2565 9.631257 TGACATGTGGTATCTCATGATTTAATT 57.369 29.630 21.70 0.69 43.64 1.40
2176 2566 9.060347 GTGACATGTGGTATCTCATGATTTAAT 57.940 33.333 21.70 1.35 43.64 1.40
2177 2567 8.046107 TGTGACATGTGGTATCTCATGATTTAA 58.954 33.333 21.70 3.88 43.64 1.52
2178 2568 7.563906 TGTGACATGTGGTATCTCATGATTTA 58.436 34.615 21.70 5.67 43.64 1.40
2179 2569 6.417258 TGTGACATGTGGTATCTCATGATTT 58.583 36.000 21.70 2.68 43.64 2.17
2180 2570 5.993055 TGTGACATGTGGTATCTCATGATT 58.007 37.500 21.70 3.35 43.64 2.57
2181 2571 5.619132 TGTGACATGTGGTATCTCATGAT 57.381 39.130 21.70 8.45 43.64 2.45
2182 2572 5.419239 TTGTGACATGTGGTATCTCATGA 57.581 39.130 21.70 0.00 43.64 3.07
2183 2573 6.688637 AATTGTGACATGTGGTATCTCATG 57.311 37.500 14.92 14.92 45.32 3.07
2184 2574 8.985315 ATTAATTGTGACATGTGGTATCTCAT 57.015 30.769 1.15 0.00 0.00 2.90
2185 2575 9.898152 TTATTAATTGTGACATGTGGTATCTCA 57.102 29.630 1.15 0.00 0.00 3.27
2187 2577 9.905713 AGTTATTAATTGTGACATGTGGTATCT 57.094 29.630 1.15 0.00 0.00 1.98
2191 2581 9.679661 TCATAGTTATTAATTGTGACATGTGGT 57.320 29.630 1.15 0.00 0.00 4.16
2267 2657 1.136891 AGCAACCTTTTGTGCAACTCC 59.863 47.619 0.00 0.00 38.04 3.85
2357 2747 7.655732 ACTCACACAAAATAAAATTTGCCTACC 59.344 33.333 0.00 0.00 42.68 3.18
2365 2755 8.006298 TCACCTCACTCACACAAAATAAAATT 57.994 30.769 0.00 0.00 0.00 1.82
2454 2844 9.982651 GCCAGTAGTCTTTATATTATCTTCACA 57.017 33.333 0.00 0.00 0.00 3.58
2461 2851 9.603189 ACCAGTAGCCAGTAGTCTTTATATTAT 57.397 33.333 0.00 0.00 0.00 1.28
2463 2853 7.916077 ACCAGTAGCCAGTAGTCTTTATATT 57.084 36.000 0.00 0.00 0.00 1.28
2476 2870 2.388735 TCATGACCTACCAGTAGCCAG 58.611 52.381 0.00 0.00 31.95 4.85
2480 2874 5.833667 TGGATACTTCATGACCTACCAGTAG 59.166 44.000 0.00 0.00 37.61 2.57
2521 2915 8.600625 CAATTTCATTTCTAAGATGCCACAATG 58.399 33.333 0.00 0.00 0.00 2.82
2535 2929 8.891671 AAATACAAGCACACAATTTCATTTCT 57.108 26.923 0.00 0.00 0.00 2.52
2563 2959 4.805140 TCCCACCATTATATGCAGGAAA 57.195 40.909 0.00 0.00 0.00 3.13
2568 2967 2.642311 ACGGATCCCACCATTATATGCA 59.358 45.455 6.06 0.00 0.00 3.96
2571 2970 4.721776 AGCATACGGATCCCACCATTATAT 59.278 41.667 6.06 0.00 0.00 0.86
2596 3014 2.632377 AGACATATCCACGTTTGCAGG 58.368 47.619 0.00 0.00 0.00 4.85
2597 3015 8.757164 TTATATAGACATATCCACGTTTGCAG 57.243 34.615 0.00 0.00 0.00 4.41
2673 3092 8.211116 TGCAAATCATTTTCAACAGAACAATT 57.789 26.923 0.00 0.00 0.00 2.32
2698 3117 8.147704 CCCACTTAACACAAAGAAAATACCATT 58.852 33.333 0.00 0.00 0.00 3.16
2699 3118 7.507616 TCCCACTTAACACAAAGAAAATACCAT 59.492 33.333 0.00 0.00 0.00 3.55
2701 3120 7.013942 ACTCCCACTTAACACAAAGAAAATACC 59.986 37.037 0.00 0.00 0.00 2.73
2702 3121 7.937649 ACTCCCACTTAACACAAAGAAAATAC 58.062 34.615 0.00 0.00 0.00 1.89
2762 3181 2.814280 TCAGACGAACCTCACTTTCC 57.186 50.000 0.00 0.00 0.00 3.13
2892 3311 5.793030 ACATATGGTAGTTACTCAGAGGC 57.207 43.478 7.80 0.00 0.00 4.70
3053 3637 6.633500 TGGTTTTCTTGGACTGATTAAGTG 57.367 37.500 0.00 0.00 40.07 3.16
3054 3638 5.241728 GCTGGTTTTCTTGGACTGATTAAGT 59.758 40.000 0.00 0.00 43.85 2.24
3213 3797 9.270640 TCCAGGAAAATATTCAACATTTTTGTG 57.729 29.630 0.00 0.00 36.09 3.33
3262 3846 9.855021 AATTGTTTTCTTATTTTCGGTATCTGG 57.145 29.630 0.00 0.00 0.00 3.86
3618 4207 7.291416 TCCTAGTTATGATATTACAGGTGCCAA 59.709 37.037 0.00 0.00 0.00 4.52
3669 4259 4.654262 TCTGGAGGTTCAGACAACTAAACT 59.346 41.667 0.00 0.00 38.70 2.66
3686 4286 0.325933 TGGCACAATCTGGTCTGGAG 59.674 55.000 0.00 0.00 31.92 3.86
3704 4304 2.435422 TGTAGGTGTGATGCATGGTTG 58.565 47.619 2.46 0.00 0.00 3.77
3716 4316 4.100963 TGTGAGACAAAGTGATGTAGGTGT 59.899 41.667 0.00 0.00 32.57 4.16
3723 4323 5.050159 TCGTCAAATGTGAGACAAAGTGATG 60.050 40.000 0.00 0.00 33.27 3.07
3749 4349 8.738645 TTTTAAAACAATTGCCACCAATTACT 57.261 26.923 5.05 0.00 46.95 2.24
3841 4457 7.391833 GTCAAAGTGGAAGAACCTCAAATATCT 59.608 37.037 0.00 0.00 39.86 1.98
3846 4462 4.594970 TGTCAAAGTGGAAGAACCTCAAA 58.405 39.130 0.00 0.00 39.86 2.69
3855 4471 1.268539 GCACCGTTGTCAAAGTGGAAG 60.269 52.381 15.31 6.11 0.00 3.46
3872 4489 4.095610 GCGAATGGTGTTTATTAGTGCAC 58.904 43.478 9.40 9.40 0.00 4.57
4051 4680 1.468914 CCGAAAAAGCTTGTCCCTAGC 59.531 52.381 0.00 0.00 38.93 3.42
4052 4681 2.742589 GTCCGAAAAAGCTTGTCCCTAG 59.257 50.000 0.00 0.00 0.00 3.02
4053 4682 2.774687 GTCCGAAAAAGCTTGTCCCTA 58.225 47.619 0.00 0.00 0.00 3.53
4054 4683 1.605753 GTCCGAAAAAGCTTGTCCCT 58.394 50.000 0.00 0.00 0.00 4.20
4055 4684 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.00 0.00 4.46
4056 4685 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
4057 4686 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
4058 4687 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
4059 4688 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
4060 4689 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
4061 4690 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
4062 4691 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
4063 4692 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
4064 4693 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
4065 4694 1.273327 GTTACTCCCTCCGTCCGAAAA 59.727 52.381 0.00 0.00 0.00 2.29
4066 4695 0.890683 GTTACTCCCTCCGTCCGAAA 59.109 55.000 0.00 0.00 0.00 3.46
4067 4696 0.251297 TGTTACTCCCTCCGTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
4068 4697 0.962356 GTGTTACTCCCTCCGTCCGA 60.962 60.000 0.00 0.00 0.00 4.55
4069 4698 0.964358 AGTGTTACTCCCTCCGTCCG 60.964 60.000 0.00 0.00 0.00 4.79
4070 4699 0.531200 CAGTGTTACTCCCTCCGTCC 59.469 60.000 0.00 0.00 0.00 4.79
4071 4700 1.542492 TCAGTGTTACTCCCTCCGTC 58.458 55.000 0.00 0.00 0.00 4.79
4072 4701 1.825474 CATCAGTGTTACTCCCTCCGT 59.175 52.381 0.00 0.00 0.00 4.69
4073 4702 1.471676 GCATCAGTGTTACTCCCTCCG 60.472 57.143 0.00 0.00 0.00 4.63
4074 4703 1.134371 GGCATCAGTGTTACTCCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
4075 4704 1.555075 TGGCATCAGTGTTACTCCCTC 59.445 52.381 0.00 0.00 0.00 4.30
4076 4705 1.656587 TGGCATCAGTGTTACTCCCT 58.343 50.000 0.00 0.00 0.00 4.20
4077 4706 2.565841 GATGGCATCAGTGTTACTCCC 58.434 52.381 22.23 0.00 0.00 4.30
4078 4707 2.171448 AGGATGGCATCAGTGTTACTCC 59.829 50.000 27.39 8.97 0.00 3.85
4079 4708 3.550437 AGGATGGCATCAGTGTTACTC 57.450 47.619 27.39 8.01 0.00 2.59
4080 4709 4.012374 CAAAGGATGGCATCAGTGTTACT 58.988 43.478 27.39 11.51 0.00 2.24
4081 4710 3.428045 GCAAAGGATGGCATCAGTGTTAC 60.428 47.826 27.39 9.41 0.00 2.50
4082 4711 2.754552 GCAAAGGATGGCATCAGTGTTA 59.245 45.455 27.39 0.00 0.00 2.41
4083 4712 1.547372 GCAAAGGATGGCATCAGTGTT 59.453 47.619 27.39 12.67 0.00 3.32
4095 4724 3.354948 TGTGCTCTGTATGCAAAGGAT 57.645 42.857 0.00 0.00 42.41 3.24
4145 4774 4.985538 ACATCCAAAAACCGTTTACACA 57.014 36.364 0.00 0.00 0.00 3.72
4214 4843 0.478072 ATGGACAGTGGCCAAGAACA 59.522 50.000 24.84 8.54 39.21 3.18
4236 4865 2.195922 GCAAGTGGAAACAAAGCAGTG 58.804 47.619 0.00 0.00 46.06 3.66
4273 4902 4.520492 ACAGAGTCAATTTTGGGACATCAC 59.480 41.667 0.00 0.00 39.30 3.06
4291 4920 5.765176 TGCTCAAAATTGTGATTCACAGAG 58.235 37.500 18.27 19.56 45.39 3.35
4293 4922 5.749588 TGTTGCTCAAAATTGTGATTCACAG 59.250 36.000 18.27 7.92 45.39 3.66
4297 4926 6.347079 CCACATGTTGCTCAAAATTGTGATTC 60.347 38.462 16.00 0.00 0.00 2.52
4384 5016 4.837972 TCATAATCGTGGTGGTTCATTCA 58.162 39.130 0.00 0.00 0.00 2.57
4386 5018 6.773976 ATTTCATAATCGTGGTGGTTCATT 57.226 33.333 0.00 0.00 0.00 2.57
4414 5050 8.721133 TGGTATCAGGTATTCAAGAGCTATTA 57.279 34.615 0.00 0.00 0.00 0.98
4594 5230 7.928307 TTACCTCTGATTCTTTCTGATTTGG 57.072 36.000 0.00 0.00 32.55 3.28


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

AutoCloner maintained by Alex Coulton.