Multiple sequence alignment - TraesCS5A01G256500

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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 TraesCS5A01G256500 chr5A 100.000 2612 0 0 1 2612 471945507 471948118 0.000000e+00 4824.0
1 TraesCS5A01G256500 chr5A 97.959 49 1 0 792 840 471946250 471946298 4.630000e-13 86.1
2 TraesCS5A01G256500 chr5A 97.959 49 1 0 744 792 471946298 471946346 4.630000e-13 86.1
3 TraesCS5A01G256500 chr5D 92.226 1698 87 24 279 1956 369427104 369428776 0.000000e+00 2362.0
4 TraesCS5A01G256500 chr5D 91.150 565 31 8 2063 2612 369428801 369429361 0.000000e+00 749.0
5 TraesCS5A01G256500 chr5D 90.526 285 16 3 1 276 369426711 369426993 1.480000e-97 366.0
6 TraesCS5A01G256500 chr5D 90.090 111 11 0 2373 2483 65990485 65990595 7.530000e-31 145.0
7 TraesCS5A01G256500 chr5D 94.915 59 0 1 792 847 369427573 369427631 3.580000e-14 89.8
8 TraesCS5A01G256500 chr5B 96.416 1116 35 5 842 1955 438556987 438558099 0.000000e+00 1834.0
9 TraesCS5A01G256500 chr5B 95.196 562 14 3 2063 2612 438558125 438558685 0.000000e+00 876.0
10 TraesCS5A01G256500 chr5B 85.981 321 39 3 347 666 438556275 438556590 3.220000e-89 339.0
11 TraesCS5A01G256500 chr5B 92.793 111 8 0 1957 2067 472663124 472663014 7.480000e-36 161.0
12 TraesCS5A01G256500 chr5B 93.069 101 7 0 2372 2472 191137757 191137857 5.820000e-32 148.0
13 TraesCS5A01G256500 chr7D 88.931 524 38 13 1011 1515 200765052 200765574 1.710000e-176 628.0
14 TraesCS5A01G256500 chr7D 79.448 326 57 9 1150 1470 578465361 578465681 3.380000e-54 222.0
15 TraesCS5A01G256500 chr7D 79.381 97 18 2 11 106 87247890 87247795 1.680000e-07 67.6
16 TraesCS5A01G256500 chr7A 88.931 524 38 13 1011 1515 214301757 214302279 1.710000e-176 628.0
17 TraesCS5A01G256500 chr7A 78.834 326 59 9 1150 1470 670536893 670537213 7.320000e-51 211.0
18 TraesCS5A01G256500 chr7A 95.652 115 4 1 1953 2067 668503054 668503167 1.600000e-42 183.0
19 TraesCS5A01G256500 chr7B 88.550 524 40 14 1011 1515 165098616 165099138 3.690000e-173 617.0
20 TraesCS5A01G256500 chr7B 93.694 111 7 0 1957 2067 508191487 508191377 1.610000e-37 167.0
21 TraesCS5A01G256500 chr4B 82.111 341 46 12 1166 1494 467717983 467718320 7.120000e-71 278.0
22 TraesCS5A01G256500 chr4A 81.525 341 48 12 1166 1494 83572035 83571698 1.540000e-67 267.0
23 TraesCS5A01G256500 chr3D 91.772 158 13 0 7 164 293193690 293193847 1.220000e-53 220.0
24 TraesCS5A01G256500 chr3D 93.939 99 6 0 2377 2475 547439634 547439732 1.620000e-32 150.0
25 TraesCS5A01G256500 chr3B 91.139 158 14 0 7 164 386525312 386525469 5.660000e-52 215.0
26 TraesCS5A01G256500 chr3A 90.566 159 14 1 7 164 386220671 386220829 2.630000e-50 209.0
27 TraesCS5A01G256500 chr6B 98.319 119 0 2 1950 2067 20696916 20697033 9.470000e-50 207.0
28 TraesCS5A01G256500 chr2D 94.643 112 6 0 1956 2067 602111636 602111525 9.610000e-40 174.0
29 TraesCS5A01G256500 chr2D 94.643 112 6 0 1956 2067 602137834 602137723 9.610000e-40 174.0
30 TraesCS5A01G256500 chr2D 93.750 112 7 0 1956 2067 602084319 602084208 4.470000e-38 169.0
31 TraesCS5A01G256500 chr2D 93.750 112 7 0 1956 2067 602182023 602181912 4.470000e-38 169.0
32 TraesCS5A01G256500 chr2D 93.137 102 7 0 2374 2475 445894879 445894980 1.620000e-32 150.0
33 TraesCS5A01G256500 chr2B 93.860 114 7 0 1956 2069 732348471 732348358 3.460000e-39 172.0
34 TraesCS5A01G256500 chr2B 100.000 31 0 0 15 45 25452635 25452605 1.010000e-04 58.4
35 TraesCS5A01G256500 chr1B 93.396 106 7 0 2378 2483 572529456 572529351 9.680000e-35 158.0
36 TraesCS5A01G256500 chr2A 93.204 103 7 0 2376 2478 587158360 587158258 4.500000e-33 152.0
37 TraesCS5A01G256500 chr4D 90.826 109 9 1 2379 2487 482704210 482704103 7.530000e-31 145.0


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 TraesCS5A01G256500 chr5A 471945507 471948118 2611 False 1665.400000 4824 98.639333 1 2612 3 chr5A.!!$F1 2611
1 TraesCS5A01G256500 chr5D 369426711 369429361 2650 False 891.700000 2362 92.204250 1 2612 4 chr5D.!!$F2 2611
2 TraesCS5A01G256500 chr5B 438556275 438558685 2410 False 1016.333333 1834 92.531000 347 2612 3 chr5B.!!$F2 2265
3 TraesCS5A01G256500 chr7D 200765052 200765574 522 False 628.000000 628 88.931000 1011 1515 1 chr7D.!!$F1 504
4 TraesCS5A01G256500 chr7A 214301757 214302279 522 False 628.000000 628 88.931000 1011 1515 1 chr7A.!!$F1 504
5 TraesCS5A01G256500 chr7B 165098616 165099138 522 False 617.000000 617 88.550000 1011 1515 1 chr7B.!!$F1 504

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
33 34 1.327764 GTGCTTAACGAGGCTATGTGC 59.672 52.381 0.0 0.0 41.94 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2446 0.107831 TTCAACTCCACCAACTCCCG 59.892 55.0 0.0 0.0 0.0 5.14 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 1.327764 GTGCTTAACGAGGCTATGTGC 59.672 52.381 0.00 0.00 41.94 4.57
53 54 4.211374 GTGCCTCAATATTAGATTCGCGTT 59.789 41.667 5.77 0.00 0.00 4.84
57 58 5.696724 CCTCAATATTAGATTCGCGTTCCTT 59.303 40.000 5.77 0.00 0.00 3.36
78 79 8.463930 TCCTTGAAAATGAAAGTACAAGATGT 57.536 30.769 0.00 0.00 37.49 3.06
89 90 6.734104 AAGTACAAGATGTGAATTGAGCTC 57.266 37.500 6.82 6.82 0.00 4.09
105 106 6.492007 TTGAGCTCAAGTTGATTTGATCTC 57.508 37.500 25.16 11.05 44.57 2.75
106 107 4.940046 TGAGCTCAAGTTGATTTGATCTCC 59.060 41.667 15.67 2.44 44.09 3.71
107 108 5.176741 AGCTCAAGTTGATTTGATCTCCT 57.823 39.130 5.91 0.00 36.55 3.69
108 109 5.568392 AGCTCAAGTTGATTTGATCTCCTT 58.432 37.500 5.91 0.00 36.55 3.36
111 112 5.551233 TCAAGTTGATTTGATCTCCTTCGT 58.449 37.500 0.08 0.00 32.39 3.85
112 113 5.409520 TCAAGTTGATTTGATCTCCTTCGTG 59.590 40.000 0.08 0.00 32.39 4.35
113 114 5.152623 AGTTGATTTGATCTCCTTCGTGA 57.847 39.130 0.00 0.00 0.00 4.35
114 115 5.738909 AGTTGATTTGATCTCCTTCGTGAT 58.261 37.500 0.00 0.00 0.00 3.06
115 116 5.583854 AGTTGATTTGATCTCCTTCGTGATG 59.416 40.000 0.00 0.00 0.00 3.07
116 117 5.343307 TGATTTGATCTCCTTCGTGATGA 57.657 39.130 0.00 0.00 0.00 2.92
131 132 2.954318 GTGATGATGCCATACAAGCCTT 59.046 45.455 0.00 0.00 32.09 4.35
181 190 6.737720 ACCTCTCTGATGCTATTAACATGA 57.262 37.500 0.00 0.00 0.00 3.07
227 237 3.839778 TGCAAAAAGGTTAACTAGGCCT 58.160 40.909 11.78 11.78 0.00 5.19
282 292 3.849619 GAACGCTCGAGATACCCTC 57.150 57.895 18.75 0.00 38.55 4.30
320 439 5.102953 TCCTCACTATGACCCAAAGATTG 57.897 43.478 0.00 0.00 0.00 2.67
338 457 4.341235 AGATTGTCCTCGATATTGACGGAA 59.659 41.667 10.88 1.29 0.00 4.30
341 460 3.889538 TGTCCTCGATATTGACGGAATCT 59.110 43.478 10.88 0.00 0.00 2.40
343 462 5.533528 TGTCCTCGATATTGACGGAATCTAA 59.466 40.000 10.88 0.00 0.00 2.10
347 466 4.219944 TCGATATTGACGGAATCTAAGGGG 59.780 45.833 0.00 0.00 0.00 4.79
357 476 3.505091 GGAATCTAAGGGGAGGCTAGGAT 60.505 52.174 0.00 0.00 0.00 3.24
398 517 7.384932 CGAAAAACCCTTGCATTTCTAAGAAAT 59.615 33.333 6.64 0.00 31.29 2.17
427 547 8.292448 ACTAATCAAAATGCACAAACTCTACAG 58.708 33.333 0.00 0.00 0.00 2.74
502 622 9.508567 GAGATAAACATGCCTTAAAACATCTTC 57.491 33.333 0.00 0.00 0.00 2.87
510 630 7.681939 TGCCTTAAAACATCTTCGAAAGTAT 57.318 32.000 0.00 0.00 0.00 2.12
644 764 3.253921 TCAAATATGCCCTCAATCATGCG 59.746 43.478 0.00 0.00 0.00 4.73
659 779 3.738399 TCATGCGCGTTGTAATGTAAAC 58.262 40.909 8.43 0.00 0.00 2.01
670 1046 6.311723 GTTGTAATGTAAACTCATTGGACCG 58.688 40.000 0.00 0.00 38.32 4.79
671 1047 4.393680 TGTAATGTAAACTCATTGGACCGC 59.606 41.667 0.00 0.00 38.32 5.68
698 1074 3.998341 GCACCATGTCAAGCAATTTGATT 59.002 39.130 0.00 0.00 46.85 2.57
700 1076 5.231702 CACCATGTCAAGCAATTTGATTCA 58.768 37.500 0.00 0.00 46.85 2.57
706 1082 7.179927 TGTCAAGCAATTTGATTCATGTTTG 57.820 32.000 0.00 8.28 46.85 2.93
708 1084 6.424509 GTCAAGCAATTTGATTCATGTTTGGA 59.575 34.615 12.46 0.00 46.85 3.53
741 1121 8.880750 AGCGTTAACTAATTTATCTCTGAAACC 58.119 33.333 3.71 0.00 0.00 3.27
795 1175 8.958119 AAGTGTGAAGATTCAGTAAGTAAACA 57.042 30.769 0.00 0.00 37.98 2.83
796 1176 8.958119 AGTGTGAAGATTCAGTAAGTAAACAA 57.042 30.769 0.00 0.00 37.98 2.83
797 1177 9.561069 AGTGTGAAGATTCAGTAAGTAAACAAT 57.439 29.630 0.00 0.00 37.98 2.71
798 1178 9.599322 GTGTGAAGATTCAGTAAGTAAACAATG 57.401 33.333 0.00 0.00 37.98 2.82
799 1179 9.337396 TGTGAAGATTCAGTAAGTAAACAATGT 57.663 29.630 0.00 0.00 37.98 2.71
810 1190 9.908152 AGTAAGTAAACAATGTTATTCCTTTGC 57.092 29.630 0.00 0.00 0.00 3.68
811 1191 9.685828 GTAAGTAAACAATGTTATTCCTTTGCA 57.314 29.630 0.00 0.00 0.00 4.08
812 1192 8.587952 AAGTAAACAATGTTATTCCTTTGCAC 57.412 30.769 0.00 0.00 0.00 4.57
813 1193 7.951591 AGTAAACAATGTTATTCCTTTGCACT 58.048 30.769 0.00 0.00 0.00 4.40
814 1194 8.421002 AGTAAACAATGTTATTCCTTTGCACTT 58.579 29.630 0.00 0.00 0.00 3.16
815 1195 9.040939 GTAAACAATGTTATTCCTTTGCACTTT 57.959 29.630 0.00 0.00 0.00 2.66
816 1196 8.504812 AAACAATGTTATTCCTTTGCACTTTT 57.495 26.923 0.00 0.00 0.00 2.27
817 1197 9.606631 AAACAATGTTATTCCTTTGCACTTTTA 57.393 25.926 0.00 0.00 0.00 1.52
818 1198 9.606631 AACAATGTTATTCCTTTGCACTTTTAA 57.393 25.926 0.00 0.00 0.00 1.52
819 1199 9.606631 ACAATGTTATTCCTTTGCACTTTTAAA 57.393 25.926 0.00 0.00 0.00 1.52
821 1201 9.830975 AATGTTATTCCTTTGCACTTTTAAAGT 57.169 25.926 4.30 4.30 44.06 2.66
864 1281 6.493166 TCTAACAAATCCACCATTTCTCCAT 58.507 36.000 0.00 0.00 31.79 3.41
870 1287 6.581388 AATCCACCATTTCTCCATAGAAGA 57.419 37.500 0.00 0.00 42.60 2.87
876 1293 7.659390 CCACCATTTCTCCATAGAAGAGATAAC 59.341 40.741 0.00 0.00 42.60 1.89
907 1325 2.433970 ACCCACAAATCCAAACACCAAG 59.566 45.455 0.00 0.00 0.00 3.61
942 1360 3.245730 TGAAAAGCATCATCCCCTTCCTT 60.246 43.478 0.00 0.00 0.00 3.36
997 1423 1.993948 AACCCTAGCTCCCCCGAAC 60.994 63.158 0.00 0.00 0.00 3.95
1416 1866 3.175240 CGCACGCTCCAGAAGTCG 61.175 66.667 0.00 0.00 0.00 4.18
1622 2072 3.006859 CCCCAGCAGTAATGTATCATCGA 59.993 47.826 0.00 0.00 0.00 3.59
1628 2078 7.978414 CCAGCAGTAATGTATCATCGATCTAAT 59.022 37.037 0.00 0.00 0.00 1.73
1644 2094 6.646653 TCGATCTAATCTTGCGCATTTCTAAT 59.353 34.615 12.75 0.00 0.00 1.73
1673 2124 3.407698 TGTGTTGTTGTTCTGTGACTGT 58.592 40.909 0.00 0.00 0.00 3.55
1679 2130 2.614057 GTTGTTCTGTGACTGTCCTTGG 59.386 50.000 5.17 0.00 0.00 3.61
1762 2213 7.424001 AGCTGTTCGGTTCTAGTATGTATTAC 58.576 38.462 0.00 0.00 0.00 1.89
1763 2214 7.067859 AGCTGTTCGGTTCTAGTATGTATTACA 59.932 37.037 0.00 0.00 32.87 2.41
1911 2362 5.844301 ATTTTCGCCTTGCATTAGTTTTG 57.156 34.783 0.00 0.00 0.00 2.44
1956 2407 7.360113 TGTGCTGTGATTACTCCATATTAGA 57.640 36.000 0.00 0.00 0.00 2.10
1957 2408 7.436933 TGTGCTGTGATTACTCCATATTAGAG 58.563 38.462 0.00 0.00 37.39 2.43
1958 2409 6.870965 GTGCTGTGATTACTCCATATTAGAGG 59.129 42.308 4.87 0.00 35.58 3.69
1959 2410 5.872070 GCTGTGATTACTCCATATTAGAGGC 59.128 44.000 4.87 0.00 35.58 4.70
1961 2412 6.084738 TGTGATTACTCCATATTAGAGGCCT 58.915 40.000 3.86 3.86 35.58 5.19
1962 2413 6.014242 TGTGATTACTCCATATTAGAGGCCTG 60.014 42.308 12.00 0.00 35.58 4.85
1963 2414 6.014156 GTGATTACTCCATATTAGAGGCCTGT 60.014 42.308 12.00 9.69 35.58 4.00
1964 2415 6.558775 TGATTACTCCATATTAGAGGCCTGTT 59.441 38.462 12.00 0.00 35.58 3.16
1965 2416 4.965200 ACTCCATATTAGAGGCCTGTTC 57.035 45.455 12.00 0.00 35.58 3.18
1966 2417 3.322254 ACTCCATATTAGAGGCCTGTTCG 59.678 47.826 12.00 0.00 35.58 3.95
1967 2418 2.632996 TCCATATTAGAGGCCTGTTCGG 59.367 50.000 12.00 2.97 0.00 4.30
1976 2427 2.190578 CCTGTTCGGCATCCCTCC 59.809 66.667 0.00 0.00 0.00 4.30
1977 2428 2.669133 CCTGTTCGGCATCCCTCCA 61.669 63.158 0.00 0.00 0.00 3.86
1978 2429 1.299648 CTGTTCGGCATCCCTCCAA 59.700 57.895 0.00 0.00 0.00 3.53
1980 2431 1.299976 GTTCGGCATCCCTCCAACT 59.700 57.895 0.00 0.00 0.00 3.16
1981 2432 0.744771 GTTCGGCATCCCTCCAACTC 60.745 60.000 0.00 0.00 0.00 3.01
1982 2433 1.910580 TTCGGCATCCCTCCAACTCC 61.911 60.000 0.00 0.00 0.00 3.85
1983 2434 2.669133 CGGCATCCCTCCAACTCCA 61.669 63.158 0.00 0.00 0.00 3.86
1984 2435 1.077429 GGCATCCCTCCAACTCCAC 60.077 63.158 0.00 0.00 0.00 4.02
1985 2436 1.450312 GCATCCCTCCAACTCCACG 60.450 63.158 0.00 0.00 0.00 4.94
1986 2437 1.450312 CATCCCTCCAACTCCACGC 60.450 63.158 0.00 0.00 0.00 5.34
1987 2438 1.613630 ATCCCTCCAACTCCACGCT 60.614 57.895 0.00 0.00 0.00 5.07
1988 2439 1.617947 ATCCCTCCAACTCCACGCTC 61.618 60.000 0.00 0.00 0.00 5.03
1989 2440 2.286523 CCCTCCAACTCCACGCTCT 61.287 63.158 0.00 0.00 0.00 4.09
1990 2441 1.216710 CCTCCAACTCCACGCTCTC 59.783 63.158 0.00 0.00 0.00 3.20
1991 2442 1.153939 CTCCAACTCCACGCTCTCG 60.154 63.158 0.00 0.00 42.43 4.04
1992 2443 2.811317 CCAACTCCACGCTCTCGC 60.811 66.667 0.00 0.00 39.84 5.03
1993 2444 2.259818 CAACTCCACGCTCTCGCT 59.740 61.111 0.00 0.00 39.84 4.93
1994 2445 1.803519 CAACTCCACGCTCTCGCTC 60.804 63.158 0.00 0.00 39.84 5.03
1995 2446 2.995872 AACTCCACGCTCTCGCTCC 61.996 63.158 0.00 0.00 39.84 4.70
1996 2447 4.544689 CTCCACGCTCTCGCTCCG 62.545 72.222 0.00 0.00 39.84 4.63
2004 2455 3.068691 TCTCGCTCCGGGAGTTGG 61.069 66.667 24.30 14.27 42.17 3.77
2005 2456 3.382832 CTCGCTCCGGGAGTTGGT 61.383 66.667 24.30 0.00 37.75 3.67
2006 2457 3.649277 CTCGCTCCGGGAGTTGGTG 62.649 68.421 24.30 11.51 37.75 4.17
2007 2458 4.760047 CGCTCCGGGAGTTGGTGG 62.760 72.222 24.30 0.00 31.39 4.61
2008 2459 3.319198 GCTCCGGGAGTTGGTGGA 61.319 66.667 24.30 0.00 31.39 4.02
2009 2460 2.982130 CTCCGGGAGTTGGTGGAG 59.018 66.667 16.15 0.00 41.82 3.86
2010 2461 1.913762 CTCCGGGAGTTGGTGGAGT 60.914 63.158 16.15 0.00 42.45 3.85
2011 2462 1.460689 TCCGGGAGTTGGTGGAGTT 60.461 57.895 0.00 0.00 0.00 3.01
2012 2463 1.302511 CCGGGAGTTGGTGGAGTTG 60.303 63.158 0.00 0.00 0.00 3.16
2013 2464 1.752198 CGGGAGTTGGTGGAGTTGA 59.248 57.895 0.00 0.00 0.00 3.18
2014 2465 0.107831 CGGGAGTTGGTGGAGTTGAA 59.892 55.000 0.00 0.00 0.00 2.69
2015 2466 1.878102 CGGGAGTTGGTGGAGTTGAAG 60.878 57.143 0.00 0.00 0.00 3.02
2016 2467 1.545651 GGGAGTTGGTGGAGTTGAAGG 60.546 57.143 0.00 0.00 0.00 3.46
2017 2468 1.143073 GGAGTTGGTGGAGTTGAAGGT 59.857 52.381 0.00 0.00 0.00 3.50
2018 2469 2.370849 GGAGTTGGTGGAGTTGAAGGTA 59.629 50.000 0.00 0.00 0.00 3.08
2019 2470 3.181448 GGAGTTGGTGGAGTTGAAGGTAA 60.181 47.826 0.00 0.00 0.00 2.85
2020 2471 4.457466 GAGTTGGTGGAGTTGAAGGTAAA 58.543 43.478 0.00 0.00 0.00 2.01
2021 2472 4.862371 AGTTGGTGGAGTTGAAGGTAAAA 58.138 39.130 0.00 0.00 0.00 1.52
2022 2473 5.265989 AGTTGGTGGAGTTGAAGGTAAAAA 58.734 37.500 0.00 0.00 0.00 1.94
2023 2474 5.359860 AGTTGGTGGAGTTGAAGGTAAAAAG 59.640 40.000 0.00 0.00 0.00 2.27
2024 2475 4.862371 TGGTGGAGTTGAAGGTAAAAAGT 58.138 39.130 0.00 0.00 0.00 2.66
2025 2476 6.003859 TGGTGGAGTTGAAGGTAAAAAGTA 57.996 37.500 0.00 0.00 0.00 2.24
2026 2477 6.059484 TGGTGGAGTTGAAGGTAAAAAGTAG 58.941 40.000 0.00 0.00 0.00 2.57
2027 2478 5.472478 GGTGGAGTTGAAGGTAAAAAGTAGG 59.528 44.000 0.00 0.00 0.00 3.18
2028 2479 5.472478 GTGGAGTTGAAGGTAAAAAGTAGGG 59.528 44.000 0.00 0.00 0.00 3.53
2029 2480 5.370289 TGGAGTTGAAGGTAAAAAGTAGGGA 59.630 40.000 0.00 0.00 0.00 4.20
2030 2481 5.938710 GGAGTTGAAGGTAAAAAGTAGGGAG 59.061 44.000 0.00 0.00 0.00 4.30
2031 2482 5.314529 AGTTGAAGGTAAAAAGTAGGGAGC 58.685 41.667 0.00 0.00 0.00 4.70
2032 2483 3.934068 TGAAGGTAAAAAGTAGGGAGCG 58.066 45.455 0.00 0.00 0.00 5.03
2033 2484 3.268330 GAAGGTAAAAAGTAGGGAGCGG 58.732 50.000 0.00 0.00 0.00 5.52
2034 2485 1.558294 AGGTAAAAAGTAGGGAGCGGG 59.442 52.381 0.00 0.00 0.00 6.13
2035 2486 1.407851 GGTAAAAAGTAGGGAGCGGGG 60.408 57.143 0.00 0.00 0.00 5.73
2036 2487 0.913924 TAAAAAGTAGGGAGCGGGGG 59.086 55.000 0.00 0.00 0.00 5.40
2037 2488 0.843343 AAAAAGTAGGGAGCGGGGGA 60.843 55.000 0.00 0.00 0.00 4.81
2038 2489 0.843343 AAAAGTAGGGAGCGGGGGAA 60.843 55.000 0.00 0.00 0.00 3.97
2039 2490 1.559965 AAAGTAGGGAGCGGGGGAAC 61.560 60.000 0.00 0.00 0.00 3.62
2040 2491 2.686106 GTAGGGAGCGGGGGAACA 60.686 66.667 0.00 0.00 0.00 3.18
2041 2492 2.365105 TAGGGAGCGGGGGAACAG 60.365 66.667 0.00 0.00 0.00 3.16
2042 2493 3.995809 TAGGGAGCGGGGGAACAGG 62.996 68.421 0.00 0.00 0.00 4.00
2044 2495 4.410400 GGAGCGGGGGAACAGGTG 62.410 72.222 0.00 0.00 0.00 4.00
2048 2499 3.322466 CGGGGGAACAGGTGCTCT 61.322 66.667 0.00 0.00 0.00 4.09
2056 2507 4.536316 CAGGTGCTCTGCAGATCC 57.464 61.111 18.63 18.77 40.08 3.36
2057 2508 1.906253 CAGGTGCTCTGCAGATCCT 59.094 57.895 18.63 20.60 40.08 3.24
2058 2509 1.117994 CAGGTGCTCTGCAGATCCTA 58.882 55.000 24.75 9.24 40.08 2.94
2059 2510 1.068895 CAGGTGCTCTGCAGATCCTAG 59.931 57.143 24.75 18.10 40.08 3.02
2060 2511 1.063341 AGGTGCTCTGCAGATCCTAGA 60.063 52.381 24.30 3.00 40.08 2.43
2061 2512 1.759445 GGTGCTCTGCAGATCCTAGAA 59.241 52.381 18.63 0.00 40.08 2.10
2103 2554 7.896383 TGTAATTAGGCCTTTGAAGCAATAT 57.104 32.000 12.58 0.00 0.00 1.28
2105 2556 6.796785 AATTAGGCCTTTGAAGCAATATGT 57.203 33.333 12.58 0.00 0.00 2.29
2204 2656 4.861196 TGTGGATAGCTAGTGTTCTCTCT 58.139 43.478 0.00 0.00 0.00 3.10
2388 2853 6.989155 AGGTCATATTTTATACTCCGTCCA 57.011 37.500 0.00 0.00 0.00 4.02
2598 3063 6.976925 GGAAATACATTCTGCATTTTCTGAGG 59.023 38.462 0.00 0.00 38.18 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 5.230942 AGGAACGCGAATCTAATATTGAGG 58.769 41.667 15.93 0.00 0.00 3.86
53 54 8.352201 CACATCTTGTACTTTCATTTTCAAGGA 58.648 33.333 0.00 0.00 34.82 3.36
78 79 6.638096 TCAAATCAACTTGAGCTCAATTCA 57.362 33.333 28.57 14.00 35.02 2.57
89 90 5.409520 TCACGAAGGAGATCAAATCAACTTG 59.590 40.000 0.00 0.00 30.90 3.16
105 106 2.837498 TGTATGGCATCATCACGAAGG 58.163 47.619 1.65 0.00 34.96 3.46
106 107 3.303593 GCTTGTATGGCATCATCACGAAG 60.304 47.826 1.65 4.89 34.96 3.79
107 108 2.613595 GCTTGTATGGCATCATCACGAA 59.386 45.455 1.65 0.00 34.96 3.85
108 109 2.212652 GCTTGTATGGCATCATCACGA 58.787 47.619 1.65 0.00 34.96 4.35
111 112 3.117776 AGAAGGCTTGTATGGCATCATCA 60.118 43.478 3.46 0.00 33.57 3.07
112 113 3.252701 CAGAAGGCTTGTATGGCATCATC 59.747 47.826 3.46 0.00 33.57 2.92
113 114 3.220110 CAGAAGGCTTGTATGGCATCAT 58.780 45.455 3.46 0.00 33.57 2.45
114 115 2.646930 CAGAAGGCTTGTATGGCATCA 58.353 47.619 3.46 0.00 33.57 3.07
115 116 1.336125 GCAGAAGGCTTGTATGGCATC 59.664 52.381 3.46 0.00 40.25 3.91
116 117 1.341285 TGCAGAAGGCTTGTATGGCAT 60.341 47.619 3.46 4.88 45.15 4.40
131 132 8.672815 TGTTACAAATATCAAAATCGATGCAGA 58.327 29.630 0.00 0.00 0.00 4.26
214 224 3.186345 GCCCAAGGCCTAGTTAACC 57.814 57.895 5.16 0.00 44.06 2.85
227 237 3.106609 TGACCCCAGTTGGCCCAA 61.107 61.111 0.00 0.00 0.00 4.12
301 420 4.536090 AGGACAATCTTTGGGTCATAGTGA 59.464 41.667 0.00 0.00 33.26 3.41
320 439 4.506886 AGATTCCGTCAATATCGAGGAC 57.493 45.455 0.00 0.00 0.00 3.85
338 457 2.828945 GCATCCTAGCCTCCCCTTAGAT 60.829 54.545 0.00 0.00 0.00 1.98
341 460 0.267658 TGCATCCTAGCCTCCCCTTA 59.732 55.000 0.00 0.00 0.00 2.69
343 462 1.132554 CATGCATCCTAGCCTCCCCT 61.133 60.000 0.00 0.00 0.00 4.79
347 466 3.887716 ACAAATTCATGCATCCTAGCCTC 59.112 43.478 0.00 0.00 0.00 4.70
357 476 4.260538 GGTTTTTCGCAACAAATTCATGCA 60.261 37.500 9.74 0.00 40.04 3.96
398 517 8.621532 AGAGTTTGTGCATTTTGATTAGTAGA 57.378 30.769 0.00 0.00 0.00 2.59
518 638 8.144478 TCCGTTTGTTTAATTCCATCAAATGAA 58.856 29.630 13.81 0.00 37.25 2.57
519 639 7.661968 TCCGTTTGTTTAATTCCATCAAATGA 58.338 30.769 13.81 0.00 37.25 2.57
638 758 3.433957 AGTTTACATTACAACGCGCATGA 59.566 39.130 18.09 0.00 0.00 3.07
644 764 5.793457 GTCCAATGAGTTTACATTACAACGC 59.207 40.000 0.00 0.00 38.25 4.84
659 779 0.597568 TGCAAAAGCGGTCCAATGAG 59.402 50.000 0.00 0.00 0.00 2.90
670 1046 1.142474 GCTTGACATGGTGCAAAAGC 58.858 50.000 0.00 0.00 33.95 3.51
671 1047 2.512485 TGCTTGACATGGTGCAAAAG 57.488 45.000 0.00 0.00 32.12 2.27
716 1092 7.844653 CGGTTTCAGAGATAAATTAGTTAACGC 59.155 37.037 0.00 0.00 0.00 4.84
717 1093 9.079833 TCGGTTTCAGAGATAAATTAGTTAACG 57.920 33.333 0.00 0.00 0.00 3.18
726 1106 8.110860 ACATTGTTTCGGTTTCAGAGATAAAT 57.889 30.769 0.00 0.00 0.00 1.40
741 1121 5.920273 AGTGCAAAGGAATAACATTGTTTCG 59.080 36.000 7.45 0.00 0.00 3.46
784 1164 9.908152 GCAAAGGAATAACATTGTTTACTTACT 57.092 29.630 7.45 3.21 0.00 2.24
785 1165 9.685828 TGCAAAGGAATAACATTGTTTACTTAC 57.314 29.630 7.45 1.00 0.00 2.34
786 1166 9.685828 GTGCAAAGGAATAACATTGTTTACTTA 57.314 29.630 7.45 0.00 0.00 2.24
787 1167 8.421002 AGTGCAAAGGAATAACATTGTTTACTT 58.579 29.630 7.45 0.12 0.00 2.24
788 1168 7.951591 AGTGCAAAGGAATAACATTGTTTACT 58.048 30.769 7.45 0.00 0.00 2.24
789 1169 8.587952 AAGTGCAAAGGAATAACATTGTTTAC 57.412 30.769 7.45 0.26 0.00 2.01
790 1170 9.606631 AAAAGTGCAAAGGAATAACATTGTTTA 57.393 25.926 7.45 0.00 0.00 2.01
791 1171 8.504812 AAAAGTGCAAAGGAATAACATTGTTT 57.495 26.923 7.45 0.00 0.00 2.83
792 1172 9.606631 TTAAAAGTGCAAAGGAATAACATTGTT 57.393 25.926 7.30 7.30 0.00 2.83
793 1173 9.606631 TTTAAAAGTGCAAAGGAATAACATTGT 57.393 25.926 0.00 0.00 0.00 2.71
795 1175 9.830975 ACTTTAAAAGTGCAAAGGAATAACATT 57.169 25.926 0.00 0.00 41.01 2.71
849 1266 5.280499 TCTCTTCTATGGAGAAATGGTGGA 58.720 41.667 0.00 0.00 41.23 4.02
864 1281 5.360144 GGTGCTGGTACTGTTATCTCTTCTA 59.640 44.000 0.00 0.00 0.00 2.10
870 1287 2.236395 GTGGGTGCTGGTACTGTTATCT 59.764 50.000 0.00 0.00 0.00 1.98
876 1293 1.812571 GATTTGTGGGTGCTGGTACTG 59.187 52.381 0.00 0.00 0.00 2.74
942 1360 2.286885 GGACTGGGGATTGGGGGA 60.287 66.667 0.00 0.00 0.00 4.81
997 1423 1.708341 GATTTGGTGGGATCCATGGG 58.292 55.000 15.23 0.00 37.33 4.00
1566 2016 2.363276 ATACTCGGGTCGGTGGCA 60.363 61.111 0.00 0.00 0.00 4.92
1622 2072 6.128445 CCGATTAGAAATGCGCAAGATTAGAT 60.128 38.462 17.11 3.45 43.02 1.98
1628 2078 2.866156 CTCCGATTAGAAATGCGCAAGA 59.134 45.455 17.11 0.00 43.02 3.02
1644 2094 3.559655 CAGAACAACAACACATTCTCCGA 59.440 43.478 0.00 0.00 28.85 4.55
1673 2124 0.395586 AGCAACAACAGCACCAAGGA 60.396 50.000 0.00 0.00 0.00 3.36
1679 2130 2.353839 CCGCAGCAACAACAGCAC 60.354 61.111 0.00 0.00 0.00 4.40
1762 2213 5.505780 TCCCCAATTACAACAATCCTACTG 58.494 41.667 0.00 0.00 0.00 2.74
1763 2214 5.340027 CCTCCCCAATTACAACAATCCTACT 60.340 44.000 0.00 0.00 0.00 2.57
1780 2231 1.836391 CAATCATACGGCCTCCCCA 59.164 57.895 0.00 0.00 0.00 4.96
1889 2340 5.296748 ACAAAACTAATGCAAGGCGAAAAT 58.703 33.333 0.00 0.00 0.00 1.82
1898 2349 9.029243 CATAGAACAACAACAAAACTAATGCAA 57.971 29.630 0.00 0.00 0.00 4.08
1911 2362 8.883731 AGCACAATACTATCATAGAACAACAAC 58.116 33.333 0.00 0.00 0.00 3.32
1959 2410 2.190578 GGAGGGATGCCGAACAGG 59.809 66.667 0.00 0.00 44.97 4.00
1961 2412 1.002624 GTTGGAGGGATGCCGAACA 60.003 57.895 0.00 0.00 0.00 3.18
1962 2413 0.744771 GAGTTGGAGGGATGCCGAAC 60.745 60.000 0.00 2.72 0.00 3.95
1963 2414 1.602237 GAGTTGGAGGGATGCCGAA 59.398 57.895 0.00 0.00 0.00 4.30
1964 2415 2.367202 GGAGTTGGAGGGATGCCGA 61.367 63.158 0.00 0.00 0.00 5.54
1965 2416 2.190578 GGAGTTGGAGGGATGCCG 59.809 66.667 0.00 0.00 0.00 5.69
1966 2417 1.077429 GTGGAGTTGGAGGGATGCC 60.077 63.158 0.00 0.00 0.00 4.40
1967 2418 1.450312 CGTGGAGTTGGAGGGATGC 60.450 63.158 0.00 0.00 0.00 3.91
1969 2420 1.613630 AGCGTGGAGTTGGAGGGAT 60.614 57.895 0.00 0.00 0.00 3.85
1970 2421 2.203788 AGCGTGGAGTTGGAGGGA 60.204 61.111 0.00 0.00 0.00 4.20
1972 2423 1.216710 GAGAGCGTGGAGTTGGAGG 59.783 63.158 0.00 0.00 0.00 4.30
1973 2424 1.153939 CGAGAGCGTGGAGTTGGAG 60.154 63.158 0.00 0.00 0.00 3.86
1974 2425 2.962569 CGAGAGCGTGGAGTTGGA 59.037 61.111 0.00 0.00 0.00 3.53
1986 2437 2.492090 CAACTCCCGGAGCGAGAG 59.508 66.667 14.86 8.02 32.04 3.20
1987 2438 3.068691 CCAACTCCCGGAGCGAGA 61.069 66.667 14.86 0.00 32.04 4.04
1988 2439 3.382832 ACCAACTCCCGGAGCGAG 61.383 66.667 14.86 3.34 32.04 5.03
1989 2440 3.691342 CACCAACTCCCGGAGCGA 61.691 66.667 14.86 0.00 32.04 4.93
1990 2441 4.760047 CCACCAACTCCCGGAGCG 62.760 72.222 14.86 5.93 32.04 5.03
1991 2442 3.316573 CTCCACCAACTCCCGGAGC 62.317 68.421 14.86 0.00 38.74 4.70
1992 2443 2.982130 CTCCACCAACTCCCGGAG 59.018 66.667 13.31 13.31 39.20 4.63
1993 2444 1.460689 AACTCCACCAACTCCCGGA 60.461 57.895 0.73 0.00 0.00 5.14
1994 2445 1.302511 CAACTCCACCAACTCCCGG 60.303 63.158 0.00 0.00 0.00 5.73
1995 2446 0.107831 TTCAACTCCACCAACTCCCG 59.892 55.000 0.00 0.00 0.00 5.14
1996 2447 1.545651 CCTTCAACTCCACCAACTCCC 60.546 57.143 0.00 0.00 0.00 4.30
1997 2448 1.143073 ACCTTCAACTCCACCAACTCC 59.857 52.381 0.00 0.00 0.00 3.85
1998 2449 2.640316 ACCTTCAACTCCACCAACTC 57.360 50.000 0.00 0.00 0.00 3.01
1999 2450 4.513406 TTTACCTTCAACTCCACCAACT 57.487 40.909 0.00 0.00 0.00 3.16
2000 2451 5.126545 ACTTTTTACCTTCAACTCCACCAAC 59.873 40.000 0.00 0.00 0.00 3.77
2001 2452 5.265989 ACTTTTTACCTTCAACTCCACCAA 58.734 37.500 0.00 0.00 0.00 3.67
2002 2453 4.862371 ACTTTTTACCTTCAACTCCACCA 58.138 39.130 0.00 0.00 0.00 4.17
2003 2454 5.472478 CCTACTTTTTACCTTCAACTCCACC 59.528 44.000 0.00 0.00 0.00 4.61
2004 2455 5.472478 CCCTACTTTTTACCTTCAACTCCAC 59.528 44.000 0.00 0.00 0.00 4.02
2005 2456 5.370289 TCCCTACTTTTTACCTTCAACTCCA 59.630 40.000 0.00 0.00 0.00 3.86
2006 2457 5.872963 TCCCTACTTTTTACCTTCAACTCC 58.127 41.667 0.00 0.00 0.00 3.85
2007 2458 5.411977 GCTCCCTACTTTTTACCTTCAACTC 59.588 44.000 0.00 0.00 0.00 3.01
2008 2459 5.314529 GCTCCCTACTTTTTACCTTCAACT 58.685 41.667 0.00 0.00 0.00 3.16
2009 2460 4.153655 CGCTCCCTACTTTTTACCTTCAAC 59.846 45.833 0.00 0.00 0.00 3.18
2010 2461 4.320870 CGCTCCCTACTTTTTACCTTCAA 58.679 43.478 0.00 0.00 0.00 2.69
2011 2462 3.307199 CCGCTCCCTACTTTTTACCTTCA 60.307 47.826 0.00 0.00 0.00 3.02
2012 2463 3.268330 CCGCTCCCTACTTTTTACCTTC 58.732 50.000 0.00 0.00 0.00 3.46
2013 2464 2.026542 CCCGCTCCCTACTTTTTACCTT 60.027 50.000 0.00 0.00 0.00 3.50
2014 2465 1.558294 CCCGCTCCCTACTTTTTACCT 59.442 52.381 0.00 0.00 0.00 3.08
2015 2466 1.407851 CCCCGCTCCCTACTTTTTACC 60.408 57.143 0.00 0.00 0.00 2.85
2016 2467 1.407851 CCCCCGCTCCCTACTTTTTAC 60.408 57.143 0.00 0.00 0.00 2.01
2017 2468 0.913924 CCCCCGCTCCCTACTTTTTA 59.086 55.000 0.00 0.00 0.00 1.52
2018 2469 0.843343 TCCCCCGCTCCCTACTTTTT 60.843 55.000 0.00 0.00 0.00 1.94
2019 2470 0.843343 TTCCCCCGCTCCCTACTTTT 60.843 55.000 0.00 0.00 0.00 2.27
2020 2471 1.229723 TTCCCCCGCTCCCTACTTT 60.230 57.895 0.00 0.00 0.00 2.66
2021 2472 1.993948 GTTCCCCCGCTCCCTACTT 60.994 63.158 0.00 0.00 0.00 2.24
2022 2473 2.365237 GTTCCCCCGCTCCCTACT 60.365 66.667 0.00 0.00 0.00 2.57
2023 2474 2.686106 TGTTCCCCCGCTCCCTAC 60.686 66.667 0.00 0.00 0.00 3.18
2024 2475 2.365105 CTGTTCCCCCGCTCCCTA 60.365 66.667 0.00 0.00 0.00 3.53
2027 2478 4.410400 CACCTGTTCCCCCGCTCC 62.410 72.222 0.00 0.00 0.00 4.70
2031 2482 3.322466 AGAGCACCTGTTCCCCCG 61.322 66.667 0.00 0.00 0.00 5.73
2032 2483 2.352805 CAGAGCACCTGTTCCCCC 59.647 66.667 0.00 0.00 38.10 5.40
2033 2484 2.360475 GCAGAGCACCTGTTCCCC 60.360 66.667 7.76 0.00 44.71 4.81
2034 2485 1.673665 CTGCAGAGCACCTGTTCCC 60.674 63.158 8.42 0.00 44.71 3.97
2035 2486 0.035630 ATCTGCAGAGCACCTGTTCC 60.036 55.000 22.96 0.00 44.71 3.62
2036 2487 1.367659 GATCTGCAGAGCACCTGTTC 58.632 55.000 26.46 10.37 44.71 3.18
2037 2488 0.035630 GGATCTGCAGAGCACCTGTT 60.036 55.000 31.24 8.15 44.71 3.16
2038 2489 0.908656 AGGATCTGCAGAGCACCTGT 60.909 55.000 31.24 8.96 44.71 4.00
2039 2490 1.068895 CTAGGATCTGCAGAGCACCTG 59.931 57.143 31.94 23.08 45.67 4.00
2040 2491 1.063341 TCTAGGATCTGCAGAGCACCT 60.063 52.381 31.24 30.15 33.79 4.00
2041 2492 1.407936 TCTAGGATCTGCAGAGCACC 58.592 55.000 31.24 25.95 33.79 5.01
2042 2493 3.749665 ATTCTAGGATCTGCAGAGCAC 57.250 47.619 31.24 20.62 33.79 4.40
2043 2494 4.162888 TGAAATTCTAGGATCTGCAGAGCA 59.837 41.667 31.24 12.67 36.92 4.26
2044 2495 4.701765 TGAAATTCTAGGATCTGCAGAGC 58.298 43.478 23.68 23.68 0.00 4.09
2045 2496 5.236911 GCTTGAAATTCTAGGATCTGCAGAG 59.763 44.000 22.96 8.09 0.00 3.35
2046 2497 5.121811 GCTTGAAATTCTAGGATCTGCAGA 58.878 41.667 20.79 20.79 0.00 4.26
2047 2498 4.880120 TGCTTGAAATTCTAGGATCTGCAG 59.120 41.667 7.63 7.63 0.00 4.41
2048 2499 4.847198 TGCTTGAAATTCTAGGATCTGCA 58.153 39.130 6.58 0.00 0.00 4.41
2049 2500 5.221009 CCTTGCTTGAAATTCTAGGATCTGC 60.221 44.000 6.58 0.00 0.00 4.26
2050 2501 5.221009 GCCTTGCTTGAAATTCTAGGATCTG 60.221 44.000 6.58 0.00 0.00 2.90
2051 2502 4.886489 GCCTTGCTTGAAATTCTAGGATCT 59.114 41.667 6.58 0.00 0.00 2.75
2052 2503 4.886489 AGCCTTGCTTGAAATTCTAGGATC 59.114 41.667 6.58 0.00 33.89 3.36
2053 2504 4.864726 AGCCTTGCTTGAAATTCTAGGAT 58.135 39.130 6.58 0.00 33.89 3.24
2054 2505 4.307032 AGCCTTGCTTGAAATTCTAGGA 57.693 40.909 6.58 0.69 33.89 2.94
2103 2554 8.006298 ACAATCAGTTTATCAAAGTTTCCACA 57.994 30.769 0.00 0.00 0.00 4.17
2388 2853 7.839680 AAAGTTGAGACACTTATTTTGGGAT 57.160 32.000 0.00 0.00 35.87 3.85
2449 2914 2.678336 CCCTCCGTCTCAAAATAAGTGC 59.322 50.000 0.00 0.00 0.00 4.40
2587 3052 7.633361 CAGTTGATTTTGACCTCAGAAAATG 57.367 36.000 0.00 0.00 33.03 2.32


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

AutoCloner maintained by Alex Coulton.