Multiple sequence alignment - TraesCS4A01G096500

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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 TraesCS4A01G096500 chr4A 100.000 3425 0 0 1 3425 104702219 104705643 0.000000e+00 6325.0
1 TraesCS4A01G096500 chr4B 90.780 2820 132 56 1 2759 444843180 444840428 0.000000e+00 3650.0
2 TraesCS4A01G096500 chr4B 87.372 586 32 15 2776 3326 444840443 444839865 4.820000e-178 634.0
3 TraesCS4A01G096500 chr4B 98.305 59 1 0 3367 3425 444839867 444839809 1.680000e-18 104.0
4 TraesCS4A01G096500 chr4D 94.850 1631 51 15 1142 2759 360100038 360098428 0.000000e+00 2516.0
5 TraesCS4A01G096500 chr4D 89.159 1153 62 34 1 1129 360101131 360100018 0.000000e+00 1378.0
6 TraesCS4A01G096500 chr4D 90.520 538 26 10 2807 3325 360098355 360097824 0.000000e+00 688.0
7 TraesCS4A01G096500 chr4D 83.678 435 52 8 1845 2271 252174760 252175183 3.200000e-105 392.0
8 TraesCS4A01G096500 chr4D 89.407 236 25 0 1845 2080 340387976 340388211 7.190000e-77 298.0
9 TraesCS4A01G096500 chr4D 96.610 59 2 0 3367 3425 360097817 360097759 7.820000e-17 99.0
10 TraesCS4A01G096500 chr4D 82.857 105 11 5 2776 2880 360098443 360098346 1.690000e-13 87.9
11 TraesCS4A01G096500 chr4D 94.118 51 2 1 3318 3368 182071809 182071760 3.670000e-10 76.8
12 TraesCS4A01G096500 chr7B 92.378 328 23 1 1583 1908 689354844 689355171 1.860000e-127 466.0
13 TraesCS4A01G096500 chr7B 87.079 356 33 10 951 1305 689339423 689339766 1.150000e-104 390.0
14 TraesCS4A01G096500 chr7B 89.655 58 5 1 3311 3368 440325588 440325644 4.740000e-09 73.1
15 TraesCS4A01G096500 chr5D 90.254 236 23 0 1845 2080 47323524 47323289 3.320000e-80 309.0
16 TraesCS4A01G096500 chr1A 82.440 336 42 7 1944 2271 577589438 577589764 9.360000e-71 278.0
17 TraesCS4A01G096500 chr1A 89.474 57 6 0 3312 3368 48977265 48977209 4.740000e-09 73.1
18 TraesCS4A01G096500 chr6A 81.306 337 45 8 1944 2271 29758437 29758764 1.220000e-64 257.0
19 TraesCS4A01G096500 chrUn 88.710 62 6 1 3307 3368 23900957 23900897 1.320000e-09 75.0
20 TraesCS4A01G096500 chr3D 92.308 52 4 0 3317 3368 450882767 450882716 1.320000e-09 75.0
21 TraesCS4A01G096500 chr2B 88.710 62 6 1 3307 3368 799161159 799161099 1.320000e-09 75.0
22 TraesCS4A01G096500 chr2B 88.710 62 6 1 3307 3368 799214315 799214255 1.320000e-09 75.0
23 TraesCS4A01G096500 chr1B 91.071 56 4 1 3313 3368 61100049 61100103 1.320000e-09 75.0
24 TraesCS4A01G096500 chr7D 89.655 58 5 1 3311 3368 47416048 47416104 4.740000e-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 TraesCS4A01G096500 chr4A 104702219 104705643 3424 False 6325.000000 6325 100.000000 1 3425 1 chr4A.!!$F1 3424
1 TraesCS4A01G096500 chr4B 444839809 444843180 3371 True 1462.666667 3650 92.152333 1 3425 3 chr4B.!!$R1 3424
2 TraesCS4A01G096500 chr4D 360097759 360101131 3372 True 953.780000 2516 90.799200 1 3425 5 chr4D.!!$R2 3424

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
988 1037 0.041312 CAGTTCTTTTCACCGCACCG 60.041 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2780 2856 0.107017 CATCCGGCCAAGTCCTTGAT 60.107 55.0 2.24 0.0 42.93 2.57 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
23 24 1.401905 CCGCTATTTGCCTGGTTCTTC 59.598 52.381 0.00 0.00 38.78 2.87
78 79 1.069500 CGTTTTCCATGGAACACGTCC 60.069 52.381 39.41 18.96 46.60 4.79
90 91 4.659172 ACGTCCGGGGGTCACGTA 62.659 66.667 15.74 0.00 44.66 3.57
136 147 0.608130 CAATGTCACGGTCTCCTCCA 59.392 55.000 0.00 0.00 0.00 3.86
153 164 3.190535 CCTCCAATTAACCCGTTGAACAG 59.809 47.826 0.00 0.00 0.00 3.16
159 170 1.594331 AACCCGTTGAACAGCTCTTC 58.406 50.000 0.00 0.00 0.00 2.87
161 172 0.250295 CCCGTTGAACAGCTCTTCCA 60.250 55.000 0.00 0.00 0.00 3.53
162 173 1.593196 CCGTTGAACAGCTCTTCCAA 58.407 50.000 0.00 0.00 0.00 3.53
163 174 1.946768 CCGTTGAACAGCTCTTCCAAA 59.053 47.619 0.00 0.00 0.00 3.28
164 175 2.554032 CCGTTGAACAGCTCTTCCAAAT 59.446 45.455 0.00 0.00 0.00 2.32
165 176 3.365364 CCGTTGAACAGCTCTTCCAAATC 60.365 47.826 0.00 0.00 0.00 2.17
166 177 3.250762 CGTTGAACAGCTCTTCCAAATCA 59.749 43.478 0.00 0.00 0.00 2.57
167 178 4.083110 CGTTGAACAGCTCTTCCAAATCAT 60.083 41.667 0.00 0.00 0.00 2.45
168 179 5.397326 GTTGAACAGCTCTTCCAAATCATC 58.603 41.667 0.00 0.00 0.00 2.92
171 188 6.417258 TGAACAGCTCTTCCAAATCATCATA 58.583 36.000 0.00 0.00 0.00 2.15
175 192 9.584008 AACAGCTCTTCCAAATCATCATATAAT 57.416 29.630 0.00 0.00 0.00 1.28
232 249 2.027745 TGCGAGGCATTCTCTTCTTCTT 60.028 45.455 0.00 0.00 40.30 2.52
233 250 2.607180 GCGAGGCATTCTCTTCTTCTTC 59.393 50.000 0.00 0.00 40.30 2.87
235 252 4.502962 CGAGGCATTCTCTTCTTCTTCTT 58.497 43.478 0.00 0.00 40.30 2.52
236 253 4.566360 CGAGGCATTCTCTTCTTCTTCTTC 59.434 45.833 0.00 0.00 40.30 2.87
237 254 5.624281 CGAGGCATTCTCTTCTTCTTCTTCT 60.624 44.000 0.00 0.00 40.30 2.85
238 255 6.125589 AGGCATTCTCTTCTTCTTCTTCTT 57.874 37.500 0.00 0.00 0.00 2.52
239 256 6.172630 AGGCATTCTCTTCTTCTTCTTCTTC 58.827 40.000 0.00 0.00 0.00 2.87
240 257 6.013466 AGGCATTCTCTTCTTCTTCTTCTTCT 60.013 38.462 0.00 0.00 0.00 2.85
241 258 6.313658 GGCATTCTCTTCTTCTTCTTCTTCTC 59.686 42.308 0.00 0.00 0.00 2.87
242 259 7.099120 GCATTCTCTTCTTCTTCTTCTTCTCT 58.901 38.462 0.00 0.00 0.00 3.10
243 260 8.250332 GCATTCTCTTCTTCTTCTTCTTCTCTA 58.750 37.037 0.00 0.00 0.00 2.43
244 261 9.793252 CATTCTCTTCTTCTTCTTCTTCTCTAG 57.207 37.037 0.00 0.00 0.00 2.43
245 262 9.753674 ATTCTCTTCTTCTTCTTCTTCTCTAGA 57.246 33.333 0.00 0.00 0.00 2.43
282 299 1.108776 CATGACAGCCATTTCCCCTG 58.891 55.000 0.00 0.00 31.94 4.45
283 300 0.685458 ATGACAGCCATTTCCCCTGC 60.685 55.000 0.00 0.00 29.34 4.85
304 325 3.100207 CCCCCTCCTGCAAGAAATAAA 57.900 47.619 0.00 0.00 34.07 1.40
306 327 3.448660 CCCCCTCCTGCAAGAAATAAAAG 59.551 47.826 0.00 0.00 34.07 2.27
308 329 4.400567 CCCCTCCTGCAAGAAATAAAAGAG 59.599 45.833 0.00 0.00 34.07 2.85
310 331 4.142293 CCTCCTGCAAGAAATAAAAGAGGC 60.142 45.833 0.00 0.00 34.07 4.70
311 332 3.763897 TCCTGCAAGAAATAAAAGAGGCC 59.236 43.478 0.00 0.00 34.07 5.19
324 345 2.776526 AGGCCAACACCCTGTCCA 60.777 61.111 5.01 0.00 0.00 4.02
383 406 1.444672 GGACGGAGGGGGTAATTCG 59.555 63.158 0.00 0.00 0.00 3.34
405 428 1.069771 GGGCGACGAAACGATGAAAAA 60.070 47.619 0.00 0.00 35.09 1.94
406 429 2.413634 GGGCGACGAAACGATGAAAAAT 60.414 45.455 0.00 0.00 35.09 1.82
407 430 2.588106 GGCGACGAAACGATGAAAAATG 59.412 45.455 0.00 0.00 35.09 2.32
449 472 2.203153 CGGTTTGATAGGGCCCGG 60.203 66.667 18.44 0.00 35.11 5.73
527 558 2.866762 CTCGCCCAATTAACTAGTGCTC 59.133 50.000 0.00 0.00 0.00 4.26
630 671 1.327690 TTCTCCATACGCCTCGCCTT 61.328 55.000 0.00 0.00 0.00 4.35
632 673 1.153449 TCCATACGCCTCGCCTTTG 60.153 57.895 0.00 0.00 0.00 2.77
651 694 1.365368 GGAGCGCTCTTGAAGGAAGC 61.365 60.000 34.46 11.99 0.00 3.86
796 839 0.387239 GCAAATGTGGCTCCGTTCAC 60.387 55.000 0.00 0.00 34.71 3.18
799 842 0.108585 AATGTGGCTCCGTTCACAGT 59.891 50.000 0.00 0.00 45.45 3.55
808 851 3.653344 CTCCGTTCACAGTTCTGATGAA 58.347 45.455 6.83 9.44 0.00 2.57
834 880 1.070914 TGCGTGTCAGTAACAATGGGA 59.929 47.619 0.00 0.00 40.31 4.37
917 966 3.433306 TGGAACTAGGAACATGGTTGG 57.567 47.619 0.00 0.00 0.00 3.77
918 967 2.041081 TGGAACTAGGAACATGGTTGGG 59.959 50.000 0.00 0.00 0.00 4.12
954 1003 0.811616 AATCGAACGGCCTGCTGATC 60.812 55.000 4.70 1.32 0.00 2.92
955 1004 1.680522 ATCGAACGGCCTGCTGATCT 61.681 55.000 4.70 0.00 0.00 2.75
978 1027 6.322201 TCTTTGATCCTTTCTGCAGTTCTTTT 59.678 34.615 14.67 0.00 0.00 2.27
979 1028 5.695851 TGATCCTTTCTGCAGTTCTTTTC 57.304 39.130 14.67 6.55 0.00 2.29
980 1029 5.132502 TGATCCTTTCTGCAGTTCTTTTCA 58.867 37.500 14.67 9.02 0.00 2.69
981 1030 4.900635 TCCTTTCTGCAGTTCTTTTCAC 57.099 40.909 14.67 0.00 0.00 3.18
982 1031 3.632145 TCCTTTCTGCAGTTCTTTTCACC 59.368 43.478 14.67 0.00 0.00 4.02
983 1032 3.548818 CCTTTCTGCAGTTCTTTTCACCG 60.549 47.826 14.67 0.00 0.00 4.94
988 1037 0.041312 CAGTTCTTTTCACCGCACCG 60.041 55.000 0.00 0.00 0.00 4.94
992 1041 2.515057 TTTTCACCGCACCGCAGT 60.515 55.556 0.00 0.00 0.00 4.40
1047 1096 1.893137 GTCCAGGACCCCAAATTTGAC 59.107 52.381 19.86 7.71 0.00 3.18
1059 1108 3.192212 CCAAATTTGACTGCCTCCTCTTC 59.808 47.826 19.86 0.00 0.00 2.87
1064 1113 1.183549 GACTGCCTCCTCTTCGGTAA 58.816 55.000 0.00 0.00 0.00 2.85
1065 1114 0.896226 ACTGCCTCCTCTTCGGTAAC 59.104 55.000 0.00 0.00 0.00 2.50
1066 1115 1.187087 CTGCCTCCTCTTCGGTAACT 58.813 55.000 0.00 0.00 0.00 2.24
1083 1133 1.465794 ACTACCTCTTCTCTGCGGAC 58.534 55.000 0.00 0.00 0.00 4.79
1184 1234 6.693315 TCCTCCTTTTACAACTCTGTTTTG 57.307 37.500 0.00 0.00 36.96 2.44
1196 1246 8.050778 ACAACTCTGTTTTGTTTACTGAATGA 57.949 30.769 0.00 0.00 33.23 2.57
1197 1247 8.519526 ACAACTCTGTTTTGTTTACTGAATGAA 58.480 29.630 0.00 0.00 33.23 2.57
1198 1248 9.520204 CAACTCTGTTTTGTTTACTGAATGAAT 57.480 29.630 0.00 0.00 0.00 2.57
1199 1249 9.520204 AACTCTGTTTTGTTTACTGAATGAATG 57.480 29.630 0.00 0.00 0.00 2.67
1303 1353 4.062293 CGTCAAGACCAACATTGAAGGTA 58.938 43.478 5.08 0.00 37.19 3.08
1332 1382 1.264045 ACCTCTCCTGCTGCTTCTCC 61.264 60.000 0.00 0.00 0.00 3.71
1430 1482 3.645687 GAGAAGCTGGGTATTGAGGAGAT 59.354 47.826 0.00 0.00 0.00 2.75
1446 1498 3.888930 AGGAGATCAAGATCGAGAACCTC 59.111 47.826 4.54 11.26 42.48 3.85
1476 1528 2.348666 GCTGTACAAGAACTATGGCACG 59.651 50.000 0.00 0.00 0.00 5.34
1574 1626 1.536284 CCGAACCATCTTCTCCTACGC 60.536 57.143 0.00 0.00 0.00 4.42
1584 1636 2.355363 TCCTACGCGTGTGTGTGC 60.355 61.111 24.59 0.00 39.65 4.57
1640 1694 1.936547 GTATTTCCTGCTTGCCTCTCG 59.063 52.381 0.00 0.00 0.00 4.04
1692 1746 3.782443 ATCAAGCCCGACCCCGTC 61.782 66.667 0.00 0.00 0.00 4.79
1802 1856 0.537188 ACTAATGGGCTCCTGACACG 59.463 55.000 0.00 0.00 0.00 4.49
1805 1859 3.612247 ATGGGCTCCTGACACGTGC 62.612 63.158 17.22 9.30 0.00 5.34
2097 2151 1.276989 CCCTTACAAGGCGGTAAGTCA 59.723 52.381 22.04 0.00 45.57 3.41
2113 2167 6.590292 CGGTAAGTCATCACAGTTTCAGTTAT 59.410 38.462 0.00 0.00 0.00 1.89
2179 2239 1.135859 ACCGTACGTCAGCTAACGAAG 60.136 52.381 18.23 6.48 45.37 3.79
2181 2241 2.164427 CGTACGTCAGCTAACGAAGTC 58.836 52.381 18.23 2.37 45.00 3.01
2182 2242 2.164427 GTACGTCAGCTAACGAAGTCG 58.836 52.381 18.23 0.11 45.00 4.18
2458 2519 0.946221 CGGTGCACCTTCAGTCTGAC 60.946 60.000 32.28 0.00 0.00 3.51
2478 2539 3.508840 CCCAAGCGCAACCCGATC 61.509 66.667 11.47 0.00 40.02 3.69
2536 2602 0.829602 TTCAGCATTGGCCGGGAAAA 60.830 50.000 2.18 0.00 42.56 2.29
2540 2606 1.815817 GCATTGGCCGGGAAAACAGT 61.816 55.000 2.18 0.00 0.00 3.55
2635 2701 4.686944 CGGGCCGGTCCTAGTATATGTATA 60.687 50.000 25.54 0.00 34.39 1.47
2636 2702 5.392125 GGGCCGGTCCTAGTATATGTATAT 58.608 45.833 20.78 0.00 34.39 0.86
2637 2703 5.243283 GGGCCGGTCCTAGTATATGTATATG 59.757 48.000 20.78 0.00 34.39 1.78
2638 2704 5.832060 GGCCGGTCCTAGTATATGTATATGT 59.168 44.000 1.90 0.00 0.00 2.29
2639 2705 7.000472 GGCCGGTCCTAGTATATGTATATGTA 59.000 42.308 1.90 0.00 0.00 2.29
2640 2706 7.040823 GGCCGGTCCTAGTATATGTATATGTAC 60.041 44.444 1.90 0.00 32.75 2.90
2641 2707 7.718753 GCCGGTCCTAGTATATGTATATGTACT 59.281 40.741 12.36 12.36 41.98 2.73
2687 2757 8.911965 GCTTGTAAATTACTACTAGTAGGAGGT 58.088 37.037 29.05 14.57 37.49 3.85
2759 2835 5.622233 GCCGAAGCAATAAATCAAGGACTTT 60.622 40.000 0.00 0.00 39.53 2.66
2760 2836 6.389906 CCGAAGCAATAAATCAAGGACTTTT 58.610 36.000 0.00 0.00 0.00 2.27
2761 2837 6.308766 CCGAAGCAATAAATCAAGGACTTTTG 59.691 38.462 0.00 0.00 0.00 2.44
2762 2838 6.183360 CGAAGCAATAAATCAAGGACTTTTGC 60.183 38.462 8.19 8.19 38.71 3.68
2763 2839 5.482006 AGCAATAAATCAAGGACTTTTGCC 58.518 37.500 11.24 0.00 39.11 4.52
2764 2840 4.631377 GCAATAAATCAAGGACTTTTGCCC 59.369 41.667 5.88 0.00 33.82 5.36
2765 2841 5.792741 CAATAAATCAAGGACTTTTGCCCA 58.207 37.500 0.00 0.00 0.00 5.36
2766 2842 6.229733 CAATAAATCAAGGACTTTTGCCCAA 58.770 36.000 0.00 0.00 0.00 4.12
2767 2843 4.769345 AAATCAAGGACTTTTGCCCAAA 57.231 36.364 0.00 0.00 0.00 3.28
2768 2844 4.769345 AATCAAGGACTTTTGCCCAAAA 57.231 36.364 6.09 6.09 37.90 2.44
2769 2845 4.769345 ATCAAGGACTTTTGCCCAAAAA 57.231 36.364 7.50 0.00 39.49 1.94
2795 2871 4.718940 AAATAAATCAAGGACTTGGCCG 57.281 40.909 11.76 0.00 40.78 6.13
2803 2879 2.106683 GGACTTGGCCGGATGAACG 61.107 63.158 5.05 0.00 0.00 3.95
2821 2954 0.102120 CGTGCATGTCTCCTCCTCTC 59.898 60.000 0.00 0.00 0.00 3.20
2830 2963 4.026744 TGTCTCCTCCTCTCAATAACTGG 58.973 47.826 0.00 0.00 0.00 4.00
2936 3086 0.034896 GGATATTCCGCGTGGATGGT 59.965 55.000 20.33 10.70 45.91 3.55
2945 3095 0.876342 GCGTGGATGGTAGTAGCAGC 60.876 60.000 9.08 9.08 0.00 5.25
2946 3096 0.459899 CGTGGATGGTAGTAGCAGCA 59.540 55.000 18.40 3.25 33.05 4.41
2947 3097 1.536922 CGTGGATGGTAGTAGCAGCAG 60.537 57.143 18.40 6.31 33.05 4.24
2948 3098 0.465705 TGGATGGTAGTAGCAGCAGC 59.534 55.000 18.40 3.75 42.56 5.25
2976 3126 1.076332 GTCGTGATACGCCAAAAGCT 58.924 50.000 0.00 0.00 42.21 3.74
3158 3314 1.035139 AGACTACAAACCGGACGTGT 58.965 50.000 9.46 11.63 0.00 4.49
3164 3320 0.303493 CAAACCGGACGTGTCACAAG 59.697 55.000 9.46 0.00 0.00 3.16
3173 3330 1.420138 ACGTGTCACAAGGGAGGAAAT 59.580 47.619 3.42 0.00 0.00 2.17
3213 3370 3.837146 TGGGTTACGGTGTAATTACCTGA 59.163 43.478 13.01 0.00 38.62 3.86
3263 3424 0.746659 GTGGACCAAACTTGCAAGCT 59.253 50.000 26.27 11.98 0.00 3.74
3294 3467 4.624452 GGGTGAGTACGACTGAAATTACAC 59.376 45.833 0.00 0.00 0.00 2.90
3300 3473 4.182693 ACGACTGAAATTACACGATGGA 57.817 40.909 0.00 0.00 0.00 3.41
3306 3479 4.450976 TGAAATTACACGATGGATCCAGG 58.549 43.478 21.33 16.53 0.00 4.45
3309 3482 0.762842 TACACGATGGATCCAGGGGG 60.763 60.000 21.33 17.21 0.00 5.40
3326 3499 8.950007 TCCAGGGGGATAATTAATTAATCAAC 57.050 34.615 11.80 5.76 38.64 3.18
3327 3500 7.953493 TCCAGGGGGATAATTAATTAATCAACC 59.047 37.037 11.80 12.91 38.64 3.77
3328 3501 7.732593 CCAGGGGGATAATTAATTAATCAACCA 59.267 37.037 11.80 0.00 35.59 3.67
3329 3502 8.585018 CAGGGGGATAATTAATTAATCAACCAC 58.415 37.037 11.80 13.76 0.00 4.16
3331 3504 8.803235 GGGGGATAATTAATTAATCAACCACTC 58.197 37.037 19.54 2.31 0.00 3.51
3332 3505 8.803235 GGGGATAATTAATTAATCAACCACTCC 58.197 37.037 11.80 10.15 0.00 3.85
3333 3506 8.803235 GGGATAATTAATTAATCAACCACTCCC 58.197 37.037 16.43 16.43 0.00 4.30
3334 3507 9.588096 GGATAATTAATTAATCAACCACTCCCT 57.412 33.333 11.80 0.00 0.00 4.20
3336 3509 7.898014 AATTAATTAATCAACCACTCCCTCC 57.102 36.000 11.08 0.00 0.00 4.30
3337 3510 3.560636 ATTAATCAACCACTCCCTCCG 57.439 47.619 0.00 0.00 0.00 4.63
3338 3511 0.539986 TAATCAACCACTCCCTCCGC 59.460 55.000 0.00 0.00 0.00 5.54
3339 3512 2.198304 AATCAACCACTCCCTCCGCC 62.198 60.000 0.00 0.00 0.00 6.13
3340 3513 4.410400 CAACCACTCCCTCCGCCC 62.410 72.222 0.00 0.00 0.00 6.13
3344 3517 2.445845 CACTCCCTCCGCCCCATA 60.446 66.667 0.00 0.00 0.00 2.74
3345 3518 2.070039 CACTCCCTCCGCCCCATAA 61.070 63.158 0.00 0.00 0.00 1.90
3346 3519 1.073706 ACTCCCTCCGCCCCATAAT 60.074 57.895 0.00 0.00 0.00 1.28
3347 3520 1.376466 CTCCCTCCGCCCCATAATG 59.624 63.158 0.00 0.00 0.00 1.90
3348 3521 1.385347 TCCCTCCGCCCCATAATGT 60.385 57.895 0.00 0.00 0.00 2.71
3349 3522 0.104882 TCCCTCCGCCCCATAATGTA 60.105 55.000 0.00 0.00 0.00 2.29
3350 3523 0.768622 CCCTCCGCCCCATAATGTAA 59.231 55.000 0.00 0.00 0.00 2.41
3351 3524 1.271379 CCCTCCGCCCCATAATGTAAG 60.271 57.143 0.00 0.00 0.00 2.34
3352 3525 1.697432 CCTCCGCCCCATAATGTAAGA 59.303 52.381 0.00 0.00 0.00 2.10
3353 3526 2.550208 CCTCCGCCCCATAATGTAAGAC 60.550 54.545 0.00 0.00 0.00 3.01
3354 3527 1.069513 TCCGCCCCATAATGTAAGACG 59.930 52.381 0.00 0.00 0.00 4.18
3355 3528 1.202604 CCGCCCCATAATGTAAGACGT 60.203 52.381 0.00 0.00 0.00 4.34
3356 3529 2.557317 CGCCCCATAATGTAAGACGTT 58.443 47.619 0.00 0.00 0.00 3.99
3357 3530 2.940410 CGCCCCATAATGTAAGACGTTT 59.060 45.455 0.00 0.00 0.00 3.60
3358 3531 3.375922 CGCCCCATAATGTAAGACGTTTT 59.624 43.478 0.00 0.00 0.00 2.43
3359 3532 4.142556 CGCCCCATAATGTAAGACGTTTTT 60.143 41.667 0.00 0.00 0.00 1.94
3405 3578 5.152097 GTTGATGCTGTGATCAAGAAAGTG 58.848 41.667 0.00 0.00 41.85 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.159135 CCAATGATCCAAAGGAAGAACCAG 59.841 45.833 0.00 0.00 42.04 4.00
23 24 2.756760 CTGTGACCCAATGATCCAAAGG 59.243 50.000 0.00 0.00 0.00 3.11
74 75 2.229690 AATTACGTGACCCCCGGACG 62.230 60.000 0.73 7.14 39.03 4.79
78 79 1.650314 GGCAAATTACGTGACCCCCG 61.650 60.000 0.00 0.00 0.00 5.73
136 147 3.751518 AGAGCTGTTCAACGGGTTAATT 58.248 40.909 1.78 0.00 34.98 1.40
175 192 6.647481 GCGTATACACATGACCCATTGTATAA 59.353 38.462 11.20 0.00 35.24 0.98
186 203 5.164090 CGATAACCATGCGTATACACATGAC 60.164 44.000 27.67 15.18 45.23 3.06
216 233 6.172630 AGAAGAAGAAGAAGAAGAGAATGCC 58.827 40.000 0.00 0.00 0.00 4.40
304 325 1.456287 GACAGGGTGTTGGCCTCTT 59.544 57.895 3.32 0.00 0.00 2.85
306 327 2.034221 GGACAGGGTGTTGGCCTC 59.966 66.667 3.32 0.00 43.36 4.70
310 331 1.073199 GGACTGGACAGGGTGTTGG 59.927 63.158 4.14 0.00 0.00 3.77
311 332 0.035458 GAGGACTGGACAGGGTGTTG 59.965 60.000 4.14 0.00 0.00 3.33
324 345 2.043450 CTCTGCCCGGAGAGGACT 60.043 66.667 0.73 0.00 45.00 3.85
383 406 3.192922 CATCGTTTCGTCGCCCCC 61.193 66.667 0.00 0.00 0.00 5.40
405 428 4.460034 GGGCAGCCATTTTTCATTTTTCAT 59.540 37.500 15.19 0.00 0.00 2.57
406 429 3.819902 GGGCAGCCATTTTTCATTTTTCA 59.180 39.130 15.19 0.00 0.00 2.69
407 430 3.191162 GGGGCAGCCATTTTTCATTTTTC 59.809 43.478 15.19 0.00 0.00 2.29
422 445 2.830186 TATCAAACCGTGGGGGCAGC 62.830 60.000 0.00 0.00 40.62 5.25
424 447 1.301623 CTATCAAACCGTGGGGGCA 59.698 57.895 0.00 0.00 40.62 5.36
449 472 2.440065 TGTCGCCCCATGATTGGC 60.440 61.111 9.94 9.94 42.15 4.52
527 558 0.886490 GTCGGGATTAGCAGCCCATG 60.886 60.000 0.00 0.00 44.94 3.66
552 583 1.901948 GGCGGGCTTAAATAGGGGC 60.902 63.158 0.00 0.00 0.00 5.80
578 609 4.718143 GGGGGAGGAGAAGAGGAG 57.282 66.667 0.00 0.00 0.00 3.69
630 671 0.396435 TTCCTTCAAGAGCGCTCCAA 59.604 50.000 32.94 21.30 0.00 3.53
632 673 1.365368 GCTTCCTTCAAGAGCGCTCC 61.365 60.000 32.94 15.76 33.29 4.70
651 694 0.682855 AGAAGGCAGAGGTCTCGAGG 60.683 60.000 13.56 0.00 34.09 4.63
799 842 0.599991 ACGCACGCAGTTCATCAGAA 60.600 50.000 0.00 0.00 41.61 3.02
808 851 3.801850 TGTTACTGACACGCACGCAGT 62.802 52.381 0.00 0.00 44.38 4.40
809 852 1.212455 TGTTACTGACACGCACGCAG 61.212 55.000 0.00 0.00 32.00 5.18
810 853 0.806492 TTGTTACTGACACGCACGCA 60.806 50.000 0.00 0.00 38.18 5.24
893 942 4.927267 ACCATGTTCCTAGTTCCATCAA 57.073 40.909 0.00 0.00 0.00 2.57
894 943 4.567537 CCAACCATGTTCCTAGTTCCATCA 60.568 45.833 0.00 0.00 0.00 3.07
895 944 3.947834 CCAACCATGTTCCTAGTTCCATC 59.052 47.826 0.00 0.00 0.00 3.51
896 945 3.309121 CCCAACCATGTTCCTAGTTCCAT 60.309 47.826 0.00 0.00 0.00 3.41
917 966 4.161001 TCGATTACTTCTCCTGGGTAAACC 59.839 45.833 0.00 0.00 40.81 3.27
918 967 5.334724 TCGATTACTTCTCCTGGGTAAAC 57.665 43.478 0.00 0.00 0.00 2.01
926 975 1.136500 GGCCGTTCGATTACTTCTCCT 59.864 52.381 0.00 0.00 0.00 3.69
954 1003 5.702349 AAGAACTGCAGAAAGGATCAAAG 57.298 39.130 23.35 0.00 0.00 2.77
955 1004 6.096705 TGAAAAGAACTGCAGAAAGGATCAAA 59.903 34.615 23.35 0.00 0.00 2.69
983 1032 3.740128 ATGATCCGGACTGCGGTGC 62.740 63.158 6.12 4.48 0.00 5.01
988 1037 0.179000 AACTCCATGATCCGGACTGC 59.821 55.000 6.12 0.00 0.00 4.40
992 1041 0.744874 GTCGAACTCCATGATCCGGA 59.255 55.000 6.61 6.61 0.00 5.14
1047 1096 1.187087 AGTTACCGAAGAGGAGGCAG 58.813 55.000 0.00 0.00 45.00 4.85
1064 1113 1.004979 AGTCCGCAGAGAAGAGGTAGT 59.995 52.381 0.00 0.00 0.00 2.73
1065 1114 1.403679 CAGTCCGCAGAGAAGAGGTAG 59.596 57.143 0.00 0.00 0.00 3.18
1066 1115 1.464734 CAGTCCGCAGAGAAGAGGTA 58.535 55.000 0.00 0.00 0.00 3.08
1114 1164 6.918892 ATTAGCGCAAAAGACACACATATA 57.081 33.333 11.47 0.00 0.00 0.86
1115 1165 5.818136 ATTAGCGCAAAAGACACACATAT 57.182 34.783 11.47 0.00 0.00 1.78
1184 1234 7.596248 ACTTGTGCATTCATTCATTCAGTAAAC 59.404 33.333 0.00 0.00 0.00 2.01
1196 1246 5.970317 TGATCAGAACTTGTGCATTCATT 57.030 34.783 0.00 0.00 0.00 2.57
1197 1247 5.417894 ACATGATCAGAACTTGTGCATTCAT 59.582 36.000 0.00 0.00 0.00 2.57
1198 1248 4.763279 ACATGATCAGAACTTGTGCATTCA 59.237 37.500 0.00 0.00 0.00 2.57
1199 1249 5.306532 ACATGATCAGAACTTGTGCATTC 57.693 39.130 0.00 0.00 0.00 2.67
1303 1353 0.031616 CAGGAGAGGTAGGAGGCCTT 60.032 60.000 6.77 0.00 36.29 4.35
1311 1361 1.408702 GAGAAGCAGCAGGAGAGGTAG 59.591 57.143 0.00 0.00 0.00 3.18
1332 1382 3.343617 AGACTGAGAAACGAGAGGAGAG 58.656 50.000 0.00 0.00 0.00 3.20
1440 1492 2.032681 AGCAGGTTGCCGAGGTTC 59.967 61.111 0.00 0.00 46.52 3.62
1446 1498 0.602638 TCTTGTACAGCAGGTTGCCG 60.603 55.000 0.00 0.00 46.52 5.69
1476 1528 4.899239 CTGAGGCCCGCCATCGTC 62.899 72.222 8.74 0.00 38.92 4.20
1500 1552 1.129251 TCGTAGTCGAAGTTGTAGCCG 59.871 52.381 0.00 0.00 43.34 5.52
1574 1626 0.586319 AAAGAATCGGCACACACACG 59.414 50.000 0.00 0.00 0.00 4.49
1584 1636 2.673368 GCAGAGTACCACAAAGAATCGG 59.327 50.000 0.00 0.00 0.00 4.18
1640 1694 1.200948 GTCTTCCATGGACAAAGCTGC 59.799 52.381 15.91 0.07 34.23 5.25
1692 1746 4.321718 TGTTCTTGAGAATCTGCTTGAGG 58.678 43.478 0.00 0.00 36.33 3.86
1784 1838 0.537188 ACGTGTCAGGAGCCCATTAG 59.463 55.000 0.00 0.00 0.00 1.73
1802 1856 4.026886 GGTGAAAATCTGAAACAAACGCAC 60.027 41.667 0.00 0.00 0.00 5.34
1805 1859 5.275695 CGTTGGTGAAAATCTGAAACAAACG 60.276 40.000 0.00 0.00 40.53 3.60
2023 2077 4.025401 CCGACGTTGGGCTTGCAC 62.025 66.667 14.66 0.00 0.00 4.57
2097 2151 8.627208 AATGTTCTGATAACTGAAACTGTGAT 57.373 30.769 0.00 0.00 36.16 3.06
2113 2167 6.821160 TGCAGGTAAATATTCGAATGTTCTGA 59.179 34.615 25.54 14.76 0.00 3.27
2134 2191 3.450578 ACACAAAACTGAAATGCTGCAG 58.549 40.909 10.11 10.11 38.10 4.41
2179 2239 0.714439 GGTAAGCAAGCGAGTTCGAC 59.286 55.000 5.60 0.00 43.02 4.20
2498 2559 2.403252 ATTCCACGTGAAGATCACCC 57.597 50.000 19.30 0.00 44.20 4.61
2536 2602 4.098044 CCTCGTGATGGATACTGTAACTGT 59.902 45.833 0.00 0.00 37.61 3.55
2540 2606 4.788679 TCTCCTCGTGATGGATACTGTAA 58.211 43.478 0.00 0.00 32.56 2.41
2635 2701 8.820933 CAAAAATCTGATCGACACATAGTACAT 58.179 33.333 0.00 0.00 0.00 2.29
2636 2702 7.201522 GCAAAAATCTGATCGACACATAGTACA 60.202 37.037 0.00 0.00 0.00 2.90
2637 2703 7.010552 AGCAAAAATCTGATCGACACATAGTAC 59.989 37.037 0.00 0.00 0.00 2.73
2638 2704 7.041721 AGCAAAAATCTGATCGACACATAGTA 58.958 34.615 0.00 0.00 0.00 1.82
2639 2705 5.877012 AGCAAAAATCTGATCGACACATAGT 59.123 36.000 0.00 0.00 0.00 2.12
2640 2706 6.355397 AGCAAAAATCTGATCGACACATAG 57.645 37.500 0.00 0.00 0.00 2.23
2641 2707 6.149308 ACAAGCAAAAATCTGATCGACACATA 59.851 34.615 0.00 0.00 0.00 2.29
2646 2712 8.452989 AATTTACAAGCAAAAATCTGATCGAC 57.547 30.769 0.00 0.00 0.00 4.20
2679 2749 9.049523 CCCGTTTTTCTTTATTATACCTCCTAC 57.950 37.037 0.00 0.00 0.00 3.18
2768 2844 9.448438 GGCCAAGTCCTTGATTTATTTTATTTT 57.552 29.630 8.59 0.00 42.93 1.82
2769 2845 7.763985 CGGCCAAGTCCTTGATTTATTTTATTT 59.236 33.333 2.24 0.00 42.93 1.40
2770 2846 7.264947 CGGCCAAGTCCTTGATTTATTTTATT 58.735 34.615 2.24 0.00 42.93 1.40
2771 2847 6.183360 CCGGCCAAGTCCTTGATTTATTTTAT 60.183 38.462 2.24 0.00 42.93 1.40
2772 2848 5.126384 CCGGCCAAGTCCTTGATTTATTTTA 59.874 40.000 2.24 0.00 42.93 1.52
2773 2849 4.081697 CCGGCCAAGTCCTTGATTTATTTT 60.082 41.667 2.24 0.00 42.93 1.82
2774 2850 3.447229 CCGGCCAAGTCCTTGATTTATTT 59.553 43.478 2.24 0.00 42.93 1.40
2775 2851 3.023832 CCGGCCAAGTCCTTGATTTATT 58.976 45.455 2.24 0.00 42.93 1.40
2776 2852 2.241176 TCCGGCCAAGTCCTTGATTTAT 59.759 45.455 2.24 0.00 42.93 1.40
2777 2853 1.631388 TCCGGCCAAGTCCTTGATTTA 59.369 47.619 2.24 0.00 42.93 1.40
2778 2854 0.404040 TCCGGCCAAGTCCTTGATTT 59.596 50.000 2.24 0.00 42.93 2.17
2779 2855 0.625849 ATCCGGCCAAGTCCTTGATT 59.374 50.000 2.24 0.00 42.93 2.57
2780 2856 0.107017 CATCCGGCCAAGTCCTTGAT 60.107 55.000 2.24 0.00 42.93 2.57
2781 2857 1.198094 TCATCCGGCCAAGTCCTTGA 61.198 55.000 2.24 0.00 42.93 3.02
2782 2858 0.322456 TTCATCCGGCCAAGTCCTTG 60.322 55.000 2.24 0.00 40.13 3.61
2783 2859 0.322546 GTTCATCCGGCCAAGTCCTT 60.323 55.000 2.24 0.00 0.00 3.36
2784 2860 1.299976 GTTCATCCGGCCAAGTCCT 59.700 57.895 2.24 0.00 0.00 3.85
2785 2861 2.106683 CGTTCATCCGGCCAAGTCC 61.107 63.158 2.24 0.00 0.00 3.85
2786 2862 1.375523 ACGTTCATCCGGCCAAGTC 60.376 57.895 2.24 0.00 0.00 3.01
2787 2863 1.671054 CACGTTCATCCGGCCAAGT 60.671 57.895 2.24 0.00 0.00 3.16
2788 2864 3.039202 GCACGTTCATCCGGCCAAG 62.039 63.158 2.24 0.00 0.00 3.61
2789 2865 3.053291 GCACGTTCATCCGGCCAA 61.053 61.111 2.24 0.00 0.00 4.52
2790 2866 3.620419 ATGCACGTTCATCCGGCCA 62.620 57.895 2.24 0.00 0.00 5.36
2795 2871 1.009829 GGAGACATGCACGTTCATCC 58.990 55.000 0.00 0.00 0.00 3.51
2803 2879 1.189752 TGAGAGGAGGAGACATGCAC 58.810 55.000 0.00 0.00 0.00 4.57
2821 2954 4.459337 GGGGTTTCAGACTTCCAGTTATTG 59.541 45.833 0.00 0.00 0.00 1.90
2830 2963 2.222027 CAGTGTGGGGTTTCAGACTTC 58.778 52.381 0.00 0.00 38.91 3.01
2945 3095 2.407521 ATCACGACGTATGCTAGCTG 57.592 50.000 17.23 3.00 0.00 4.24
2946 3096 2.096367 CGTATCACGACGTATGCTAGCT 60.096 50.000 17.23 4.07 46.05 3.32
2947 3097 2.231693 CGTATCACGACGTATGCTAGC 58.768 52.381 8.10 8.10 46.05 3.42
2948 3098 2.231693 GCGTATCACGACGTATGCTAG 58.768 52.381 0.00 0.00 46.05 3.42
2976 3126 5.708230 CCAAAGGCACAAATAAGTAGTGGTA 59.292 40.000 0.00 0.00 33.98 3.25
3158 3314 2.026636 CCCGTAATTTCCTCCCTTGTGA 60.027 50.000 0.00 0.00 0.00 3.58
3213 3370 4.081420 AGACGATGCTGACTTACCAGAAAT 60.081 41.667 0.00 0.00 36.29 2.17
3263 3424 2.575279 AGTCGTACTCACCCTTCTCCTA 59.425 50.000 0.00 0.00 0.00 2.94
3306 3479 8.803235 GGAGTGGTTGATTAATTAATTATCCCC 58.197 37.037 19.69 12.79 0.00 4.81
3317 3490 2.421529 GCGGAGGGAGTGGTTGATTAAT 60.422 50.000 0.00 0.00 0.00 1.40
3327 3500 1.418908 ATTATGGGGCGGAGGGAGTG 61.419 60.000 0.00 0.00 0.00 3.51
3328 3501 1.073706 ATTATGGGGCGGAGGGAGT 60.074 57.895 0.00 0.00 0.00 3.85
3329 3502 1.376466 CATTATGGGGCGGAGGGAG 59.624 63.158 0.00 0.00 0.00 4.30
3331 3504 0.768622 TTACATTATGGGGCGGAGGG 59.231 55.000 0.00 0.00 0.00 4.30
3332 3505 1.697432 TCTTACATTATGGGGCGGAGG 59.303 52.381 0.00 0.00 0.00 4.30
3333 3506 2.767505 GTCTTACATTATGGGGCGGAG 58.232 52.381 0.00 0.00 0.00 4.63
3334 3507 1.069513 CGTCTTACATTATGGGGCGGA 59.930 52.381 0.00 0.00 0.00 5.54
3335 3508 1.202604 ACGTCTTACATTATGGGGCGG 60.203 52.381 11.76 0.00 0.00 6.13
3336 3509 2.234300 ACGTCTTACATTATGGGGCG 57.766 50.000 0.00 2.66 0.00 6.13
3337 3510 4.976224 AAAACGTCTTACATTATGGGGC 57.024 40.909 0.00 0.00 0.00 5.80
3363 3536 9.810231 GCATCAACAAACCATTTTTAATTAGTG 57.190 29.630 0.00 0.00 0.00 2.74
3364 3537 9.777297 AGCATCAACAAACCATTTTTAATTAGT 57.223 25.926 0.00 0.00 0.00 2.24
3405 3578 1.414527 GCTCTTCTCCGCACGCTAAC 61.415 60.000 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.