Multiple sequence alignment - TraesCS5D01G297100

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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 TraesCS5D01G297100 chr5D 100.000 3309 0 0 1 3309 393996441 393993133 0.000000e+00 6111.0
1 TraesCS5D01G297100 chr5A 86.949 2766 169 83 105 2758 496012750 496010065 0.000000e+00 2931.0
2 TraesCS5D01G297100 chr5A 94.444 72 4 0 1 72 496012813 496012742 9.710000e-21 111.0
3 TraesCS5D01G297100 chr5B 91.976 1857 85 29 489 2316 473873237 473871416 0.000000e+00 2545.0
4 TraesCS5D01G297100 chr5B 91.368 950 59 13 2363 3309 473871334 473870405 0.000000e+00 1279.0
5 TraesCS5D01G297100 chr5B 75.949 237 18 21 96 313 473873487 473873271 5.880000e-13 86.1
6 TraesCS5D01G297100 chr7A 78.912 588 95 17 1352 1932 254897402 254897967 4.030000e-99 372.0
7 TraesCS5D01G297100 chr7B 78.547 592 93 22 1352 1932 218548777 218548209 3.140000e-95 359.0
8 TraesCS5D01G297100 chr7D 82.292 384 64 4 1352 1733 242784689 242784308 2.460000e-86 329.0
9 TraesCS5D01G297100 chr6D 86.517 89 8 4 1383 1469 455251636 455251722 9.780000e-16 95.3


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 TraesCS5D01G297100 chr5D 393993133 393996441 3308 True 6111.000000 6111 100.0000 1 3309 1 chr5D.!!$R1 3308
1 TraesCS5D01G297100 chr5A 496010065 496012813 2748 True 1521.000000 2931 90.6965 1 2758 2 chr5A.!!$R1 2757
2 TraesCS5D01G297100 chr5B 473870405 473873487 3082 True 1303.366667 2545 86.4310 96 3309 3 chr5B.!!$R1 3213
3 TraesCS5D01G297100 chr7A 254897402 254897967 565 False 372.000000 372 78.9120 1352 1932 1 chr7A.!!$F1 580
4 TraesCS5D01G297100 chr7B 218548209 218548777 568 True 359.000000 359 78.5470 1352 1932 1 chr7B.!!$R1 580


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
75 76 0.031817 TACCTGCCTACCTGTACCCC 60.032 60.0 0.00 0.0 0.00 4.95 F
79 80 0.117541 TGCCTACCTGTACCCCTCAA 59.882 55.0 0.00 0.0 0.00 3.02 F
359 383 0.456221 GGACGACTCATGGACGATGT 59.544 55.0 11.45 0.0 33.29 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 2189 0.109153 TTCGGGAGCTGCATGCATAT 59.891 50.000 22.97 12.96 45.94 1.78 R
2022 2190 0.815213 GTTCGGGAGCTGCATGCATA 60.815 55.000 22.97 0.00 45.94 3.14 R
2316 2484 1.519234 TGCGTGCATCGGTCATCTC 60.519 57.895 10.02 0.00 40.26 2.75 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
45 46 3.372206 CACTCGCTGCAAGTTTTAGCTAT 59.628 43.478 0.00 0.00 35.36 2.97
53 54 8.271157 GCTGCAAGTTTTAGCTATCAGCTTCA 62.271 42.308 5.92 0.00 43.27 3.02
66 67 3.371087 GCTTCAGCTACCTGCCTAC 57.629 57.895 0.00 0.00 44.23 3.18
67 68 0.179070 GCTTCAGCTACCTGCCTACC 60.179 60.000 0.00 0.00 44.23 3.18
68 69 1.490574 CTTCAGCTACCTGCCTACCT 58.509 55.000 0.00 0.00 44.23 3.08
69 70 1.137872 CTTCAGCTACCTGCCTACCTG 59.862 57.143 0.00 0.00 44.23 4.00
70 71 0.041238 TCAGCTACCTGCCTACCTGT 59.959 55.000 0.00 0.00 44.23 4.00
71 72 1.286849 TCAGCTACCTGCCTACCTGTA 59.713 52.381 0.00 0.00 44.23 2.74
72 73 1.409427 CAGCTACCTGCCTACCTGTAC 59.591 57.143 0.00 0.00 44.23 2.90
73 74 0.751452 GCTACCTGCCTACCTGTACC 59.249 60.000 0.00 0.00 35.15 3.34
74 75 1.411041 CTACCTGCCTACCTGTACCC 58.589 60.000 0.00 0.00 0.00 3.69
75 76 0.031817 TACCTGCCTACCTGTACCCC 60.032 60.000 0.00 0.00 0.00 4.95
76 77 1.003051 CCTGCCTACCTGTACCCCT 59.997 63.158 0.00 0.00 0.00 4.79
77 78 1.049289 CCTGCCTACCTGTACCCCTC 61.049 65.000 0.00 0.00 0.00 4.30
78 79 0.325296 CTGCCTACCTGTACCCCTCA 60.325 60.000 0.00 0.00 0.00 3.86
79 80 0.117541 TGCCTACCTGTACCCCTCAA 59.882 55.000 0.00 0.00 0.00 3.02
80 81 1.282382 GCCTACCTGTACCCCTCAAA 58.718 55.000 0.00 0.00 0.00 2.69
81 82 1.631898 GCCTACCTGTACCCCTCAAAA 59.368 52.381 0.00 0.00 0.00 2.44
82 83 2.040679 GCCTACCTGTACCCCTCAAAAA 59.959 50.000 0.00 0.00 0.00 1.94
164 171 6.507900 CGGGATAAACGATAGCATCATATCT 58.492 40.000 0.00 0.00 42.67 1.98
165 172 6.980978 CGGGATAAACGATAGCATCATATCTT 59.019 38.462 0.00 0.00 42.67 2.40
166 173 7.043125 CGGGATAAACGATAGCATCATATCTTG 60.043 40.741 0.00 0.00 42.67 3.02
167 174 7.766278 GGGATAAACGATAGCATCATATCTTGT 59.234 37.037 0.00 0.00 42.67 3.16
201 208 0.841289 TGGATCAGAGCATGCATCCA 59.159 50.000 25.76 25.76 40.40 3.41
253 273 1.677576 ACCATGGCATTGTTATCGCAG 59.322 47.619 13.04 0.00 0.00 5.18
258 278 1.004927 GGCATTGTTATCGCAGACGTC 60.005 52.381 7.70 7.70 42.51 4.34
265 285 4.413969 TGTTATCGCAGACGTCGATTTTA 58.586 39.130 14.70 1.90 43.27 1.52
268 288 2.937591 TCGCAGACGTCGATTTTAACT 58.062 42.857 10.46 0.00 41.18 2.24
322 345 4.985538 ACATATATACTAGAGCCGTGCC 57.014 45.455 0.00 0.00 0.00 5.01
326 349 6.605995 ACATATATACTAGAGCCGTGCCATAA 59.394 38.462 0.00 0.00 0.00 1.90
327 350 3.662247 ATACTAGAGCCGTGCCATAAC 57.338 47.619 0.00 0.00 0.00 1.89
341 365 4.024893 GTGCCATAACACGACAAGATATGG 60.025 45.833 5.89 5.89 36.85 2.74
351 375 3.977579 CGACAAGATATGGACGACTCATG 59.022 47.826 0.00 0.00 35.86 3.07
359 383 0.456221 GGACGACTCATGGACGATGT 59.544 55.000 11.45 0.00 33.29 3.06
371 395 6.734137 TCATGGACGATGTTTAAAATATGGC 58.266 36.000 0.00 0.00 33.29 4.40
373 397 4.035792 TGGACGATGTTTAAAATATGGCCG 59.964 41.667 0.00 0.00 0.00 6.13
414 438 4.830765 CGGGCCGCTGGATTTCGA 62.831 66.667 15.42 0.00 0.00 3.71
448 472 1.101635 CAGGCACCAGGATCATGCAG 61.102 60.000 0.73 0.00 41.27 4.41
465 489 3.927552 GCAGGAAGCAGTTTCGTATAC 57.072 47.619 0.00 0.00 44.79 1.47
505 546 2.284190 GGTTAGTAGCCTCGACGTACT 58.716 52.381 0.00 0.00 0.00 2.73
541 587 6.250527 GTGGAATTAATGTACATGCACGTTTC 59.749 38.462 9.63 7.26 0.00 2.78
668 722 3.942748 GGTAATGTCCAAACGGAATGCTA 59.057 43.478 0.00 0.00 33.16 3.49
820 874 7.901752 GGAATTCCACTACGTACTCGTCGTC 62.902 52.000 20.04 0.00 42.46 4.20
833 887 1.403323 TCGTCGTCGTAGAGCTAGAGA 59.597 52.381 1.33 0.00 36.95 3.10
837 893 2.629137 TCGTCGTAGAGCTAGAGAGGAT 59.371 50.000 0.00 0.00 36.95 3.24
843 899 2.081043 AGAGCTAGAGAGGATGGGGAT 58.919 52.381 0.00 0.00 0.00 3.85
850 906 2.451294 AGGATGGGGATGGGCTCC 60.451 66.667 0.00 0.00 44.11 4.70
871 927 3.699538 CCCCTGCTGCTATATATACACGA 59.300 47.826 0.00 0.00 0.00 4.35
883 939 8.464404 GCTATATATACACGACTTGTTCCCATA 58.536 37.037 0.00 0.00 39.91 2.74
886 942 2.253610 ACACGACTTGTTCCCATAGGA 58.746 47.619 0.00 0.00 41.88 2.94
922 1004 1.203313 ACTGCCTTCCTTCCCTAGTCA 60.203 52.381 0.00 0.00 0.00 3.41
947 1029 3.433740 GGGAAGGAGAAGAACACACAGTT 60.434 47.826 0.00 0.00 44.93 3.16
983 1070 2.649331 TCTGCTTAGTTACCGTGCTC 57.351 50.000 0.00 0.00 0.00 4.26
1108 1202 3.119637 TGCTCAACTGTTGATGCATCATG 60.120 43.478 29.13 22.60 38.20 3.07
1181 1276 3.945285 ACACAAAGTGTCATTTCTCCGTT 59.055 39.130 0.00 0.00 43.92 4.44
1184 1279 3.771577 AAGTGTCATTTCTCCGTTCCT 57.228 42.857 0.00 0.00 0.00 3.36
1185 1280 3.045601 AGTGTCATTTCTCCGTTCCTG 57.954 47.619 0.00 0.00 0.00 3.86
1230 1325 1.738099 CTTCCTGGTGTTCCTCGCG 60.738 63.158 0.00 0.00 34.23 5.87
1273 1368 3.188460 TCGAGCACCTTAATCTTTTGCAC 59.812 43.478 0.00 0.00 35.57 4.57
1276 1371 2.351738 GCACCTTAATCTTTTGCACGCT 60.352 45.455 0.00 0.00 33.24 5.07
1304 1399 3.569277 TGTTGTGATCACCATGAGTTTGG 59.431 43.478 22.85 0.00 42.82 3.28
1501 1645 0.537143 TGCTCACCATCAACGCCTTT 60.537 50.000 0.00 0.00 0.00 3.11
1753 1897 6.482898 AGTACTACTACTACTGCTGCTCTA 57.517 41.667 0.00 0.00 30.81 2.43
1793 1940 7.068348 GGACCATGAGATCTACAGTAACTAACA 59.932 40.741 0.00 0.00 0.00 2.41
1797 1944 6.188407 TGAGATCTACAGTAACTAACAGGCT 58.812 40.000 0.00 0.00 0.00 4.58
1913 2062 0.460311 CCGTCGCCTGGTTCTTCTAT 59.540 55.000 0.00 0.00 0.00 1.98
1956 2109 1.324718 CGTCACCGTACGTCTTCTTG 58.675 55.000 15.21 0.00 38.07 3.02
1972 2132 5.855395 GTCTTCTTGCACAATCAGTTTCATC 59.145 40.000 0.00 0.00 0.00 2.92
1973 2133 4.408993 TCTTGCACAATCAGTTTCATCG 57.591 40.909 0.00 0.00 0.00 3.84
1975 2143 3.811722 TGCACAATCAGTTTCATCGTC 57.188 42.857 0.00 0.00 0.00 4.20
1977 2145 3.187022 TGCACAATCAGTTTCATCGTCAG 59.813 43.478 0.00 0.00 0.00 3.51
1982 2150 6.476706 CACAATCAGTTTCATCGTCAGCTATA 59.523 38.462 0.00 0.00 0.00 1.31
1983 2151 7.170489 CACAATCAGTTTCATCGTCAGCTATAT 59.830 37.037 0.00 0.00 0.00 0.86
1992 2160 4.655762 TCGTCAGCTATATATCCATGGC 57.344 45.455 6.96 0.00 32.92 4.40
1996 2164 5.625426 CGTCAGCTATATATCCATGGCACTT 60.625 44.000 6.96 0.00 35.04 3.16
2002 2170 6.696148 GCTATATATCCATGGCACTTACGTAC 59.304 42.308 6.96 0.00 32.99 3.67
2007 2175 2.671396 CCATGGCACTTACGTACTTGAC 59.329 50.000 0.00 0.00 0.00 3.18
2008 2176 3.585862 CATGGCACTTACGTACTTGACT 58.414 45.455 9.35 0.00 0.00 3.41
2009 2177 3.293311 TGGCACTTACGTACTTGACTC 57.707 47.619 9.35 0.00 0.00 3.36
2012 2180 3.243336 GCACTTACGTACTTGACTCCTG 58.757 50.000 0.00 0.00 0.00 3.86
2013 2181 3.305199 GCACTTACGTACTTGACTCCTGT 60.305 47.826 0.00 0.00 0.00 4.00
2014 2182 4.227538 CACTTACGTACTTGACTCCTGTG 58.772 47.826 0.00 0.00 0.00 3.66
2015 2183 3.887716 ACTTACGTACTTGACTCCTGTGT 59.112 43.478 0.00 0.00 0.00 3.72
2016 2184 5.049198 CACTTACGTACTTGACTCCTGTGTA 60.049 44.000 0.00 0.00 0.00 2.90
2017 2185 5.532406 ACTTACGTACTTGACTCCTGTGTAA 59.468 40.000 0.00 0.00 0.00 2.41
2018 2186 4.924305 ACGTACTTGACTCCTGTGTAAA 57.076 40.909 0.00 0.00 0.00 2.01
2019 2187 5.266733 ACGTACTTGACTCCTGTGTAAAA 57.733 39.130 0.00 0.00 0.00 1.52
2020 2188 5.045872 ACGTACTTGACTCCTGTGTAAAAC 58.954 41.667 0.00 0.00 0.00 2.43
2021 2189 5.045215 CGTACTTGACTCCTGTGTAAAACA 58.955 41.667 0.00 0.00 37.22 2.83
2022 2190 5.694910 CGTACTTGACTCCTGTGTAAAACAT 59.305 40.000 0.00 0.00 38.39 2.71
2023 2191 6.864685 CGTACTTGACTCCTGTGTAAAACATA 59.135 38.462 0.00 0.00 38.39 2.29
2024 2192 7.544566 CGTACTTGACTCCTGTGTAAAACATAT 59.455 37.037 0.00 0.00 38.39 1.78
2025 2193 7.672983 ACTTGACTCCTGTGTAAAACATATG 57.327 36.000 0.00 0.00 38.39 1.78
2026 2194 6.149474 ACTTGACTCCTGTGTAAAACATATGC 59.851 38.462 1.58 0.00 38.39 3.14
2059 2227 1.599797 CGTGGGCGGGTTCTTCTTT 60.600 57.895 0.00 0.00 0.00 2.52
2316 2484 1.863454 CAAGGCTTTCTGATCCGATCG 59.137 52.381 8.51 8.51 0.00 3.69
2319 2487 1.338337 GGCTTTCTGATCCGATCGAGA 59.662 52.381 18.66 12.67 0.00 4.04
2320 2488 2.029470 GGCTTTCTGATCCGATCGAGAT 60.029 50.000 18.66 16.99 0.00 2.75
2321 2489 2.985809 GCTTTCTGATCCGATCGAGATG 59.014 50.000 18.66 8.37 0.00 2.90
2322 2490 3.304996 GCTTTCTGATCCGATCGAGATGA 60.305 47.826 18.66 10.74 0.00 2.92
2324 2492 2.155279 TCTGATCCGATCGAGATGACC 58.845 52.381 18.66 6.73 0.00 4.02
2350 2518 3.813143 CACGGGCGCATGCATTCA 61.813 61.111 19.57 0.00 45.35 2.57
2351 2519 3.511595 ACGGGCGCATGCATTCAG 61.512 61.111 19.57 9.26 45.35 3.02
2353 2521 2.829914 GGGCGCATGCATTCAGGA 60.830 61.111 19.57 0.00 45.35 3.86
2354 2522 2.719979 GGCGCATGCATTCAGGAG 59.280 61.111 19.57 0.00 45.35 3.69
2355 2523 1.820906 GGCGCATGCATTCAGGAGA 60.821 57.895 19.57 0.00 45.35 3.71
2356 2524 1.170919 GGCGCATGCATTCAGGAGAT 61.171 55.000 19.57 0.00 45.35 2.75
2357 2525 0.040336 GCGCATGCATTCAGGAGATG 60.040 55.000 19.57 0.00 42.15 2.90
2358 2526 1.589803 CGCATGCATTCAGGAGATGA 58.410 50.000 19.57 0.00 35.62 2.92
2371 2574 6.106648 TCAGGAGATGAATCAATCGCTAAT 57.893 37.500 0.00 0.00 34.02 1.73
2448 2658 4.681025 TCGTTCGTTTGTAATGGTCTGTAC 59.319 41.667 0.00 0.00 0.00 2.90
2459 2669 5.584253 AATGGTCTGTACTAGTAGCACAG 57.416 43.478 20.46 20.46 40.21 3.66
2516 2726 2.478033 CCGGCCGGGCAAGTAATTC 61.478 63.158 37.42 0.00 0.00 2.17
2525 2735 4.196193 CGGGCAAGTAATTCATCTACCAA 58.804 43.478 0.00 0.00 0.00 3.67
2616 2828 3.487574 GCGAACTGATACTGCACTATGTC 59.512 47.826 0.00 0.00 0.00 3.06
2628 2840 2.096496 GCACTATGTCTGTTGCATGTCC 59.904 50.000 0.00 0.00 0.00 4.02
2692 2914 1.460504 CACAATGCATGAGAGGTGCT 58.539 50.000 0.00 0.00 42.92 4.40
2707 2929 3.368822 GCTTGTGGCATGGAAGCA 58.631 55.556 18.47 0.00 41.48 3.91
2727 2949 2.360475 GAGTGGGAGTTGGCTGGC 60.360 66.667 0.00 0.00 0.00 4.85
2742 2964 0.537188 CTGGCTGGTCGGAGTACAAT 59.463 55.000 0.00 0.00 0.00 2.71
2781 3004 3.766068 ATCAGAGATGCCCACATACAG 57.234 47.619 0.00 0.00 36.35 2.74
2798 3021 5.045942 ACATACAGACACATACATTCACCCA 60.046 40.000 0.00 0.00 0.00 4.51
2799 3022 4.574674 ACAGACACATACATTCACCCAT 57.425 40.909 0.00 0.00 0.00 4.00
2800 3023 5.692115 ACAGACACATACATTCACCCATA 57.308 39.130 0.00 0.00 0.00 2.74
2801 3024 6.252599 ACAGACACATACATTCACCCATAT 57.747 37.500 0.00 0.00 0.00 1.78
2802 3025 7.373617 ACAGACACATACATTCACCCATATA 57.626 36.000 0.00 0.00 0.00 0.86
2803 3026 7.801104 ACAGACACATACATTCACCCATATAA 58.199 34.615 0.00 0.00 0.00 0.98
2804 3027 8.271458 ACAGACACATACATTCACCCATATAAA 58.729 33.333 0.00 0.00 0.00 1.40
2805 3028 9.288576 CAGACACATACATTCACCCATATAAAT 57.711 33.333 0.00 0.00 0.00 1.40
2813 3036 8.995027 ACATTCACCCATATAAATACACACAT 57.005 30.769 0.00 0.00 0.00 3.21
2819 3042 8.556194 CACCCATATAAATACACACATACACAC 58.444 37.037 0.00 0.00 0.00 3.82
2820 3043 8.268605 ACCCATATAAATACACACATACACACA 58.731 33.333 0.00 0.00 0.00 3.72
2836 3059 3.969976 ACACACACTATCCCTATGAGCAT 59.030 43.478 0.00 0.00 0.00 3.79
2840 3063 5.011533 ACACACTATCCCTATGAGCATCTTC 59.988 44.000 0.00 0.00 34.92 2.87
2846 3069 4.155709 TCCCTATGAGCATCTTCGAGATT 58.844 43.478 0.00 0.00 31.32 2.40
2847 3070 4.021632 TCCCTATGAGCATCTTCGAGATTG 60.022 45.833 0.00 0.00 31.32 2.67
2848 3071 3.679025 CCTATGAGCATCTTCGAGATTGC 59.321 47.826 7.28 7.28 31.32 3.56
2862 3085 3.585862 GAGATTGCCTTGTAGTCGACAA 58.414 45.455 19.50 2.93 46.03 3.18
2880 3103 4.336101 GACAAAAACATGTTCGTCGACAA 58.664 39.130 17.16 6.36 32.57 3.18
2884 3107 3.854286 AACATGTTCGTCGACAAAGTC 57.146 42.857 17.16 1.59 32.47 3.01
2899 3122 0.946221 AAGTCGAAGCTGCTTGGTCG 60.946 55.000 21.25 17.25 0.00 4.79
2901 3124 1.069090 TCGAAGCTGCTTGGTCGTT 59.931 52.632 21.25 0.00 0.00 3.85
2912 3136 1.084935 TTGGTCGTTGACGTGTGTGG 61.085 55.000 0.00 0.00 40.80 4.17
2919 3143 2.542597 GTTGACGTGTGTGGTTGACTA 58.457 47.619 0.00 0.00 0.00 2.59
2948 3172 4.778415 CCGACACAGGCCTCGACG 62.778 72.222 13.28 13.78 31.24 5.12
2986 3210 2.159558 GCACTTCAGTAGTCGTCGATGA 60.160 50.000 2.39 2.39 33.85 2.92
3008 3232 0.319641 GAGTCGAAGTCGCCCTTTGT 60.320 55.000 0.00 0.00 39.60 2.83
3014 3238 1.705997 AAGTCGCCCTTTGTGGAGGT 61.706 55.000 0.00 0.00 38.35 3.85
3015 3239 1.966451 GTCGCCCTTTGTGGAGGTG 60.966 63.158 0.00 0.00 38.35 4.00
3149 3373 7.237173 GTCAATTAATTGGACAACTCTCTTCG 58.763 38.462 24.40 0.00 38.30 3.79
3156 3380 3.134081 TGGACAACTCTCTTCGACCTTTT 59.866 43.478 0.00 0.00 0.00 2.27
3193 3417 2.432444 CTAAGGGACCGCATTTCAACA 58.568 47.619 0.00 0.00 0.00 3.33
3194 3418 1.698506 AAGGGACCGCATTTCAACAA 58.301 45.000 0.00 0.00 0.00 2.83
3195 3419 1.698506 AGGGACCGCATTTCAACAAA 58.301 45.000 0.00 0.00 0.00 2.83
3196 3420 2.035632 AGGGACCGCATTTCAACAAAA 58.964 42.857 0.00 0.00 0.00 2.44
3234 3458 3.023832 CCACCAAACAAGACTTGAACCT 58.976 45.455 21.95 0.00 0.00 3.50
3235 3459 3.181487 CCACCAAACAAGACTTGAACCTG 60.181 47.826 21.95 11.59 0.00 4.00
3257 3482 2.165030 GTGGGCTGATTCCATCACAAAG 59.835 50.000 0.00 0.00 36.58 2.77
3278 3503 8.734386 ACAAAGAAATCTAACCATCTAAGCAAG 58.266 33.333 0.00 0.00 0.00 4.01
3280 3505 5.825151 AGAAATCTAACCATCTAAGCAAGGC 59.175 40.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 1.688627 GGTACAGGTAGGCAGGTAGCT 60.689 57.143 0.00 0.00 44.79 3.32
60 61 0.117541 TTGAGGGGTACAGGTAGGCA 59.882 55.000 0.00 0.00 0.00 4.75
86 87 5.068591 CAGGTAGTAGGCAGGTTTTGTTTTT 59.931 40.000 0.00 0.00 0.00 1.94
87 88 4.583073 CAGGTAGTAGGCAGGTTTTGTTTT 59.417 41.667 0.00 0.00 0.00 2.43
88 89 4.142038 CAGGTAGTAGGCAGGTTTTGTTT 58.858 43.478 0.00 0.00 0.00 2.83
89 90 3.137728 ACAGGTAGTAGGCAGGTTTTGTT 59.862 43.478 0.00 0.00 0.00 2.83
90 91 2.709397 ACAGGTAGTAGGCAGGTTTTGT 59.291 45.455 0.00 0.00 0.00 2.83
91 92 3.418684 ACAGGTAGTAGGCAGGTTTTG 57.581 47.619 0.00 0.00 0.00 2.44
92 93 4.820894 CTACAGGTAGTAGGCAGGTTTT 57.179 45.455 0.00 0.00 45.28 2.43
164 171 1.358877 CATCGATCGCCAACAGACAA 58.641 50.000 11.09 0.00 0.00 3.18
165 172 0.460109 CCATCGATCGCCAACAGACA 60.460 55.000 11.09 0.00 0.00 3.41
166 173 0.179111 TCCATCGATCGCCAACAGAC 60.179 55.000 11.09 0.00 0.00 3.51
167 174 0.752658 ATCCATCGATCGCCAACAGA 59.247 50.000 11.09 1.49 0.00 3.41
192 199 2.027325 CATCACCGGTGGATGCATG 58.973 57.895 33.40 23.95 36.12 4.06
201 208 2.045926 GAGCCTTGCATCACCGGT 60.046 61.111 0.00 0.00 0.00 5.28
249 269 2.779969 GCAGTTAAAATCGACGTCTGCG 60.780 50.000 14.70 0.70 44.93 5.18
253 273 6.089150 ACTTTAGAGCAGTTAAAATCGACGTC 59.911 38.462 5.18 5.18 0.00 4.34
265 285 8.507249 CAGCACTTAAATTACTTTAGAGCAGTT 58.493 33.333 0.00 0.00 0.00 3.16
268 288 7.979444 ACAGCACTTAAATTACTTTAGAGCA 57.021 32.000 0.00 0.00 0.00 4.26
282 305 3.992643 TGTACGCCTTTACAGCACTTAA 58.007 40.909 0.00 0.00 0.00 1.85
322 345 5.173312 GTCGTCCATATCTTGTCGTGTTATG 59.827 44.000 0.00 0.00 0.00 1.90
326 349 2.753452 AGTCGTCCATATCTTGTCGTGT 59.247 45.455 0.00 0.00 0.00 4.49
327 350 3.181500 TGAGTCGTCCATATCTTGTCGTG 60.181 47.826 0.00 0.00 0.00 4.35
335 359 2.552743 TCGTCCATGAGTCGTCCATATC 59.447 50.000 0.00 0.00 0.00 1.63
341 365 2.279582 AACATCGTCCATGAGTCGTC 57.720 50.000 0.00 0.00 36.21 4.20
351 375 4.533222 CGGCCATATTTTAAACATCGTCC 58.467 43.478 2.24 0.00 0.00 4.79
359 383 4.641094 ACGAATGTCCGGCCATATTTTAAA 59.359 37.500 0.00 0.00 0.00 1.52
371 395 1.526887 GATGTATGCACGAATGTCCGG 59.473 52.381 0.00 0.00 0.00 5.14
373 397 1.526887 CCGATGTATGCACGAATGTCC 59.473 52.381 0.00 0.00 0.00 4.02
414 438 1.019673 GCCTGATGAATGCACGACAT 58.980 50.000 0.00 0.00 42.30 3.06
448 472 4.666237 AGTACGTATACGAAACTGCTTCC 58.334 43.478 30.77 5.72 43.02 3.46
465 489 5.025986 ACCAAAGCATAAAACGAAGTACG 57.974 39.130 0.00 0.00 45.00 3.67
569 615 0.179108 GCACGTAGCCTCTACAAGGG 60.179 60.000 0.00 0.00 46.32 3.95
645 699 2.490115 GCATTCCGTTTGGACATTACCA 59.510 45.455 0.00 0.00 46.45 3.25
668 722 3.313526 GCCAAGATGAAGAATACGTGCAT 59.686 43.478 0.00 0.00 0.00 3.96
820 874 2.432444 CCCATCCTCTCTAGCTCTACG 58.568 57.143 0.00 0.00 0.00 3.51
821 875 2.377193 TCCCCATCCTCTCTAGCTCTAC 59.623 54.545 0.00 0.00 0.00 2.59
822 876 2.719676 TCCCCATCCTCTCTAGCTCTA 58.280 52.381 0.00 0.00 0.00 2.43
833 887 2.451294 GGAGCCCATCCCCATCCT 60.451 66.667 0.00 0.00 43.01 3.24
850 906 4.399618 AGTCGTGTATATATAGCAGCAGGG 59.600 45.833 0.00 0.00 0.00 4.45
851 907 5.568685 AGTCGTGTATATATAGCAGCAGG 57.431 43.478 0.00 0.00 0.00 4.85
854 910 6.308282 GGAACAAGTCGTGTATATATAGCAGC 59.692 42.308 0.00 0.00 40.60 5.25
922 1004 3.138283 TGTGTGTTCTTCTCCTTCCCAAT 59.862 43.478 0.00 0.00 0.00 3.16
947 1029 7.892771 ACTAAGCAGATCAGATGGATGTATCTA 59.107 37.037 0.00 0.00 35.70 1.98
1108 1202 3.859443 TGGTTTGGAAATACATGCATGC 58.141 40.909 26.53 11.82 0.00 4.06
1259 1354 4.154918 AGGAGAAGCGTGCAAAAGATTAAG 59.845 41.667 0.00 0.00 0.00 1.85
1273 1368 1.728971 GTGATCACAACAGGAGAAGCG 59.271 52.381 21.07 0.00 0.00 4.68
1276 1371 3.678289 CATGGTGATCACAACAGGAGAA 58.322 45.455 26.47 1.72 46.61 2.87
1753 1897 3.584406 TCATGGTCCTGATCACTCAAACT 59.416 43.478 0.00 0.00 0.00 2.66
1793 1940 0.466189 CATTATTCACCGGCCAGCCT 60.466 55.000 0.00 0.00 0.00 4.58
1797 1944 1.031235 CATGCATTATTCACCGGCCA 58.969 50.000 0.00 0.00 0.00 5.36
1913 2062 1.059584 TGTCCTTGGTGAAGAGGCCA 61.060 55.000 5.01 0.00 32.93 5.36
1956 2109 3.740590 CTGACGATGAAACTGATTGTGC 58.259 45.455 0.00 0.00 0.00 4.57
1972 2132 4.115516 GTGCCATGGATATATAGCTGACG 58.884 47.826 18.40 0.00 0.00 4.35
1973 2133 5.350504 AGTGCCATGGATATATAGCTGAC 57.649 43.478 18.40 0.00 0.00 3.51
1975 2143 5.750547 CGTAAGTGCCATGGATATATAGCTG 59.249 44.000 18.40 0.00 0.00 4.24
1996 2164 6.183360 TGTTTTACACAGGAGTCAAGTACGTA 60.183 38.462 0.00 0.00 0.00 3.57
2002 2170 6.149308 TGCATATGTTTTACACAGGAGTCAAG 59.851 38.462 4.29 0.00 39.40 3.02
2007 2175 5.163632 TGCATGCATATGTTTTACACAGGAG 60.164 40.000 18.46 0.00 39.40 3.69
2008 2176 4.704057 TGCATGCATATGTTTTACACAGGA 59.296 37.500 18.46 0.00 39.40 3.86
2009 2177 4.996344 TGCATGCATATGTTTTACACAGG 58.004 39.130 18.46 0.00 39.40 4.00
2012 2180 4.675510 AGCTGCATGCATATGTTTTACAC 58.324 39.130 22.97 0.00 45.94 2.90
2013 2181 4.202040 GGAGCTGCATGCATATGTTTTACA 60.202 41.667 22.97 0.00 45.94 2.41
2014 2182 4.293415 GGAGCTGCATGCATATGTTTTAC 58.707 43.478 22.97 5.44 45.94 2.01
2015 2183 3.318839 GGGAGCTGCATGCATATGTTTTA 59.681 43.478 22.97 0.00 45.94 1.52
2016 2184 2.101917 GGGAGCTGCATGCATATGTTTT 59.898 45.455 22.97 1.63 45.94 2.43
2017 2185 1.684983 GGGAGCTGCATGCATATGTTT 59.315 47.619 22.97 3.13 45.94 2.83
2018 2186 1.325355 GGGAGCTGCATGCATATGTT 58.675 50.000 22.97 7.76 45.94 2.71
2019 2187 0.887836 CGGGAGCTGCATGCATATGT 60.888 55.000 22.97 5.86 45.94 2.29
2020 2188 0.604511 TCGGGAGCTGCATGCATATG 60.605 55.000 22.97 11.19 45.94 1.78
2021 2189 0.109153 TTCGGGAGCTGCATGCATAT 59.891 50.000 22.97 12.96 45.94 1.78
2022 2190 0.815213 GTTCGGGAGCTGCATGCATA 60.815 55.000 22.97 0.00 45.94 3.14
2023 2191 2.117156 GTTCGGGAGCTGCATGCAT 61.117 57.895 22.97 7.28 45.94 3.96
2024 2192 2.747460 GTTCGGGAGCTGCATGCA 60.747 61.111 21.29 21.29 45.94 3.96
2025 2193 3.869272 CGTTCGGGAGCTGCATGC 61.869 66.667 11.82 11.82 43.29 4.06
2026 2194 2.434884 ACGTTCGGGAGCTGCATG 60.435 61.111 7.79 0.00 0.00 4.06
2050 2218 2.351777 GGCCACCCCAAAGAAGAAC 58.648 57.895 0.00 0.00 0.00 3.01
2316 2484 1.519234 TGCGTGCATCGGTCATCTC 60.519 57.895 10.02 0.00 40.26 2.75
2319 2487 3.188100 CGTGCGTGCATCGGTCAT 61.188 61.111 0.00 0.00 40.26 3.06
2348 2516 5.535753 TTAGCGATTGATTCATCTCCTGA 57.464 39.130 0.00 0.00 0.00 3.86
2350 2518 6.106648 TCATTAGCGATTGATTCATCTCCT 57.893 37.500 0.00 0.00 0.00 3.69
2351 2519 6.981762 ATCATTAGCGATTGATTCATCTCC 57.018 37.500 0.00 0.00 0.00 3.71
2371 2574 2.433491 CGGTCGGTTCGCCAATCA 60.433 61.111 0.00 0.00 37.00 2.57
2459 2669 0.296642 GACGACAACACACACACGAC 59.703 55.000 0.00 0.00 0.00 4.34
2468 2678 0.106149 AGACCCTTGGACGACAACAC 59.894 55.000 0.00 0.00 34.76 3.32
2469 2679 0.105964 CAGACCCTTGGACGACAACA 59.894 55.000 0.00 0.00 34.76 3.33
2514 2724 2.627945 GCACGTGGATTGGTAGATGAA 58.372 47.619 18.88 0.00 0.00 2.57
2516 2726 1.299541 GGCACGTGGATTGGTAGATG 58.700 55.000 18.88 0.00 0.00 2.90
2616 2828 0.813184 GGGACATGGACATGCAACAG 59.187 55.000 11.96 0.00 42.39 3.16
2628 2840 2.223021 CGTGCGAATAAACAGGGACATG 60.223 50.000 0.00 0.00 0.00 3.21
2692 2914 0.178967 TCCTTGCTTCCATGCCACAA 60.179 50.000 0.00 0.00 0.00 3.33
2707 2929 1.763770 CAGCCAACTCCCACTCCTT 59.236 57.895 0.00 0.00 0.00 3.36
2755 2978 2.092968 TGTGGGCATCTCTGATTGTACC 60.093 50.000 0.00 0.00 0.00 3.34
2764 2987 2.169352 GTGTCTGTATGTGGGCATCTCT 59.831 50.000 0.00 0.00 36.58 3.10
2800 3023 9.542462 GGATAGTGTGTGTATGTGTGTATTTAT 57.458 33.333 0.00 0.00 0.00 1.40
2801 3024 7.982919 GGGATAGTGTGTGTATGTGTGTATTTA 59.017 37.037 0.00 0.00 0.00 1.40
2802 3025 6.821665 GGGATAGTGTGTGTATGTGTGTATTT 59.178 38.462 0.00 0.00 0.00 1.40
2803 3026 6.156256 AGGGATAGTGTGTGTATGTGTGTATT 59.844 38.462 0.00 0.00 0.00 1.89
2804 3027 5.661312 AGGGATAGTGTGTGTATGTGTGTAT 59.339 40.000 0.00 0.00 0.00 2.29
2805 3028 5.020795 AGGGATAGTGTGTGTATGTGTGTA 58.979 41.667 0.00 0.00 0.00 2.90
2813 3036 4.542697 TGCTCATAGGGATAGTGTGTGTA 58.457 43.478 0.00 0.00 0.00 2.90
2814 3037 3.374764 TGCTCATAGGGATAGTGTGTGT 58.625 45.455 0.00 0.00 0.00 3.72
2819 3042 4.460731 TCGAAGATGCTCATAGGGATAGTG 59.539 45.833 0.00 0.00 0.00 2.74
2820 3043 4.667573 TCGAAGATGCTCATAGGGATAGT 58.332 43.478 0.00 0.00 0.00 2.12
2836 3059 3.427638 CGACTACAAGGCAATCTCGAAGA 60.428 47.826 0.00 0.00 0.00 2.87
2840 3063 2.186076 GTCGACTACAAGGCAATCTCG 58.814 52.381 8.70 0.00 0.00 4.04
2862 3085 4.584394 GACTTTGTCGACGAACATGTTTT 58.416 39.130 14.37 2.72 0.00 2.43
2880 3103 0.946221 CGACCAAGCAGCTTCGACTT 60.946 55.000 4.07 0.00 33.20 3.01
2884 3107 1.205064 CAACGACCAAGCAGCTTCG 59.795 57.895 12.50 12.50 37.50 3.79
2899 3122 1.365699 AGTCAACCACACACGTCAAC 58.634 50.000 0.00 0.00 0.00 3.18
2901 3124 3.462483 AATAGTCAACCACACACGTCA 57.538 42.857 0.00 0.00 0.00 4.35
2912 3136 2.475200 GCCGATGCCAAATAGTCAAC 57.525 50.000 0.00 0.00 0.00 3.18
2936 3160 2.660258 AAACAAGCGTCGAGGCCTGT 62.660 55.000 24.51 24.51 39.17 4.00
2948 3172 1.661509 GCCTTCACCGCAAACAAGC 60.662 57.895 0.00 0.00 0.00 4.01
2972 3196 2.873472 GACTCCATCATCGACGACTACT 59.127 50.000 0.00 0.00 0.00 2.57
2975 3199 0.658368 CGACTCCATCATCGACGACT 59.342 55.000 0.00 0.00 40.86 4.18
3008 3232 1.221566 CATCGCCATCACACCTCCA 59.778 57.895 0.00 0.00 0.00 3.86
3014 3238 1.447663 CGGTGTCATCGCCATCACA 60.448 57.895 0.00 0.00 43.79 3.58
3015 3239 2.173669 CCGGTGTCATCGCCATCAC 61.174 63.158 0.00 0.00 43.79 3.06
3079 3303 3.035503 CGCCCGCAAAAACAAGGC 61.036 61.111 0.00 0.00 40.33 4.35
3122 3346 6.464222 AGAGAGTTGTCCAATTAATTGACGA 58.536 36.000 26.32 18.46 40.14 4.20
3126 3350 7.237173 GTCGAAGAGAGTTGTCCAATTAATTG 58.763 38.462 19.40 19.40 36.95 2.32
3133 3357 2.317040 AGGTCGAAGAGAGTTGTCCAA 58.683 47.619 0.00 0.00 36.95 3.53
3156 3380 4.387437 CCCTTAGGGCCTGATCCATTAAAA 60.387 45.833 18.53 0.00 35.35 1.52
3170 3394 1.076995 AAATGCGGTCCCTTAGGGC 60.077 57.895 13.54 7.82 43.94 5.19
3172 3396 1.743394 GTTGAAATGCGGTCCCTTAGG 59.257 52.381 0.00 0.00 0.00 2.69
3257 3482 5.825151 AGCCTTGCTTAGATGGTTAGATTTC 59.175 40.000 0.00 0.00 33.89 2.17
3278 3503 2.416972 CCTTGTACTCGTGGACTAAGCC 60.417 54.545 0.93 0.00 0.00 4.35
3280 3505 2.731341 CGCCTTGTACTCGTGGACTAAG 60.731 54.545 0.93 3.77 0.00 2.18
3284 3509 0.172803 ATCGCCTTGTACTCGTGGAC 59.827 55.000 0.00 0.00 0.00 4.02
3285 3510 0.172578 CATCGCCTTGTACTCGTGGA 59.827 55.000 0.00 0.00 0.00 4.02
3286 3511 1.421410 GCATCGCCTTGTACTCGTGG 61.421 60.000 0.00 0.00 0.00 4.94
3287 3512 0.458543 AGCATCGCCTTGTACTCGTG 60.459 55.000 0.00 0.00 0.00 4.35
3288 3513 0.246635 AAGCATCGCCTTGTACTCGT 59.753 50.000 0.00 0.00 0.00 4.18
3289 3514 2.203800 TAAGCATCGCCTTGTACTCG 57.796 50.000 0.00 0.00 0.00 4.18



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

AutoCloner maintained by Alex Coulton.