Multiple sequence alignment - TraesCS2A01G054000

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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 TraesCS2A01G054000 chr2A 100.000 2414 0 0 1 2414 22119305 22121718 0.000000e+00 4458.0
1 TraesCS2A01G054000 chr2A 98.942 189 1 1 2226 2414 22111157 22111344 1.070000e-88 337.0
2 TraesCS2A01G054000 chr2A 95.699 186 8 0 2226 2411 22112754 22112939 1.400000e-77 300.0
3 TraesCS2A01G054000 chr6A 96.322 870 25 2 1362 2226 389560668 389559801 0.000000e+00 1423.0
4 TraesCS2A01G054000 chr6A 97.436 39 1 0 2160 2198 12926568 12926530 1.550000e-07 67.6
5 TraesCS2A01G054000 chr4A 94.521 876 39 5 1360 2229 24872215 24871343 0.000000e+00 1343.0
6 TraesCS2A01G054000 chr2B 91.104 888 57 3 469 1355 34236129 34236995 0.000000e+00 1182.0
7 TraesCS2A01G054000 chr2B 91.071 280 11 7 174 442 34235736 34236012 1.360000e-97 366.0
8 TraesCS2A01G054000 chr7D 84.625 761 69 21 1357 2100 13686577 13687306 0.000000e+00 713.0
9 TraesCS2A01G054000 chr7D 82.877 292 35 8 1942 2227 588830814 588830532 5.150000e-62 248.0
10 TraesCS2A01G054000 chr7D 84.000 175 25 3 1358 1531 588831541 588831369 5.340000e-37 165.0
11 TraesCS2A01G054000 chr3B 78.193 830 89 40 1359 2166 664024773 664025532 1.700000e-121 446.0
12 TraesCS2A01G054000 chr7B 84.444 360 41 10 1519 1875 4982976 4982629 8.270000e-90 340.0
13 TraesCS2A01G054000 chr3D 76.846 596 88 17 1650 2227 606504213 606504776 8.440000e-75 291.0
14 TraesCS2A01G054000 chr3D 76.520 592 85 18 1650 2228 468949043 468948493 8.500000e-70 274.0
15 TraesCS2A01G054000 chr3D 76.401 589 84 20 1650 2225 468965902 468965356 1.420000e-67 267.0
16 TraesCS2A01G054000 chr3D 81.818 176 21 8 1359 1531 468949521 468949354 1.160000e-28 137.0
17 TraesCS2A01G054000 chr3D 81.818 176 21 8 1359 1531 468966381 468966214 1.160000e-28 137.0
18 TraesCS2A01G054000 chr1D 82.443 262 23 12 1359 1618 52348457 52348217 8.750000e-50 207.0
19 TraesCS2A01G054000 chr1D 92.453 53 3 1 2151 2202 169061294 169061242 9.260000e-10 75.0
20 TraesCS2A01G054000 chr3A 86.207 174 21 3 1359 1531 694868455 694868284 4.100000e-43 185.0
21 TraesCS2A01G054000 chr3A 80.460 174 24 6 1359 1531 747055287 747055451 9.060000e-25 124.0
22 TraesCS2A01G054000 chr3A 85.321 109 13 2 2124 2229 137915807 137915915 2.540000e-20 110.0
23 TraesCS2A01G054000 chr1A 86.111 72 8 2 2151 2220 225510518 225510447 2.570000e-10 76.8
24 TraesCS2A01G054000 chr1B 92.000 50 3 1 2151 2199 249629213 249629262 4.310000e-08 69.4
25 TraesCS2A01G054000 chr5B 97.436 39 1 0 2160 2198 704770961 704770923 1.550000e-07 67.6
26 TraesCS2A01G054000 chr2D 97.436 39 1 0 2160 2198 137576214 137576252 1.550000e-07 67.6


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 TraesCS2A01G054000 chr2A 22119305 22121718 2413 False 4458.0 4458 100.0000 1 2414 1 chr2A.!!$F1 2413
1 TraesCS2A01G054000 chr2A 22111157 22112939 1782 False 318.5 337 97.3205 2226 2414 2 chr2A.!!$F2 188
2 TraesCS2A01G054000 chr6A 389559801 389560668 867 True 1423.0 1423 96.3220 1362 2226 1 chr6A.!!$R2 864
3 TraesCS2A01G054000 chr4A 24871343 24872215 872 True 1343.0 1343 94.5210 1360 2229 1 chr4A.!!$R1 869
4 TraesCS2A01G054000 chr2B 34235736 34236995 1259 False 774.0 1182 91.0875 174 1355 2 chr2B.!!$F1 1181
5 TraesCS2A01G054000 chr7D 13686577 13687306 729 False 713.0 713 84.6250 1357 2100 1 chr7D.!!$F1 743
6 TraesCS2A01G054000 chr7D 588830532 588831541 1009 True 206.5 248 83.4385 1358 2227 2 chr7D.!!$R1 869
7 TraesCS2A01G054000 chr3B 664024773 664025532 759 False 446.0 446 78.1930 1359 2166 1 chr3B.!!$F1 807
8 TraesCS2A01G054000 chr3D 606504213 606504776 563 False 291.0 291 76.8460 1650 2227 1 chr3D.!!$F1 577
9 TraesCS2A01G054000 chr3D 468948493 468949521 1028 True 205.5 274 79.1690 1359 2228 2 chr3D.!!$R1 869
10 TraesCS2A01G054000 chr3D 468965356 468966381 1025 True 202.0 267 79.1095 1359 2225 2 chr3D.!!$R2 866

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
243 244 0.247460 GCAGCCCCACCTTTTCATTC 59.753 55.000 0.00 0.00 0.0 2.67 F
415 427 1.003839 GTTCATCCTGCCGTGGTCA 60.004 57.895 0.00 0.00 0.0 4.02 F
1279 1382 0.678048 GGTCCCGAATGAAGCTGCTT 60.678 55.000 15.92 15.92 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1128 1231 0.458669 GCAGCAGGAACCCATTCATG 59.541 55.0 0.0 0.0 46.96 3.07 R
1338 1441 0.599204 TGTGGAGCCGACGAAACTTC 60.599 55.0 0.0 0.0 0.00 3.01 R
2290 2658 0.939419 AACCACGTTTAACCAGTCGC 59.061 50.0 0.0 0.0 0.00 5.19 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
20 21 2.057316 CTAGCTCTGACGTATGCATGC 58.943 52.381 11.82 11.82 0.00 4.06
21 22 0.873312 AGCTCTGACGTATGCATGCG 60.873 55.000 31.52 31.52 41.71 4.73
32 33 2.507547 GCATGCGTGCCATTGTGG 60.508 61.111 20.59 0.00 45.76 4.17
33 34 2.182284 CATGCGTGCCATTGTGGG 59.818 61.111 0.00 0.00 38.19 4.61
48 49 3.951775 TGTGGGCACAAATTAATGTCC 57.048 42.857 0.00 5.70 41.24 4.02
49 50 2.230025 TGTGGGCACAAATTAATGTCCG 59.770 45.455 0.00 0.00 43.98 4.79
50 51 2.490115 GTGGGCACAAATTAATGTCCGA 59.510 45.455 0.00 0.00 43.98 4.55
51 52 2.490115 TGGGCACAAATTAATGTCCGAC 59.510 45.455 7.73 0.00 43.98 4.79
52 53 2.752903 GGGCACAAATTAATGTCCGACT 59.247 45.455 0.00 0.00 29.23 4.18
53 54 3.181500 GGGCACAAATTAATGTCCGACTC 60.181 47.826 0.00 0.00 29.23 3.36
54 55 3.181500 GGCACAAATTAATGTCCGACTCC 60.181 47.826 0.00 0.00 0.00 3.85
55 56 3.689649 GCACAAATTAATGTCCGACTCCT 59.310 43.478 0.00 0.00 0.00 3.69
56 57 4.156008 GCACAAATTAATGTCCGACTCCTT 59.844 41.667 0.00 0.00 0.00 3.36
57 58 5.335661 GCACAAATTAATGTCCGACTCCTTT 60.336 40.000 0.00 0.00 0.00 3.11
58 59 6.677913 CACAAATTAATGTCCGACTCCTTTT 58.322 36.000 0.00 0.00 0.00 2.27
59 60 7.145323 CACAAATTAATGTCCGACTCCTTTTT 58.855 34.615 0.00 0.00 0.00 1.94
60 61 8.293867 CACAAATTAATGTCCGACTCCTTTTTA 58.706 33.333 0.00 0.00 0.00 1.52
61 62 9.020731 ACAAATTAATGTCCGACTCCTTTTTAT 57.979 29.630 0.00 0.00 0.00 1.40
97 98 2.616634 CAGGAGCACTGCTATGTCAT 57.383 50.000 2.71 0.00 39.88 3.06
98 99 2.481854 CAGGAGCACTGCTATGTCATC 58.518 52.381 2.71 0.00 39.88 2.92
99 100 2.102757 CAGGAGCACTGCTATGTCATCT 59.897 50.000 2.71 0.00 39.88 2.90
100 101 3.320256 CAGGAGCACTGCTATGTCATCTA 59.680 47.826 2.71 0.00 39.88 1.98
101 102 4.021280 CAGGAGCACTGCTATGTCATCTAT 60.021 45.833 2.71 0.00 39.88 1.98
102 103 5.184671 CAGGAGCACTGCTATGTCATCTATA 59.815 44.000 2.71 0.00 39.88 1.31
103 104 5.777223 AGGAGCACTGCTATGTCATCTATAA 59.223 40.000 2.71 0.00 39.88 0.98
104 105 6.071447 AGGAGCACTGCTATGTCATCTATAAG 60.071 42.308 2.71 0.00 39.88 1.73
105 106 6.035368 AGCACTGCTATGTCATCTATAAGG 57.965 41.667 0.21 0.00 36.99 2.69
106 107 5.777223 AGCACTGCTATGTCATCTATAAGGA 59.223 40.000 0.21 0.00 36.99 3.36
107 108 6.071447 AGCACTGCTATGTCATCTATAAGGAG 60.071 42.308 0.21 0.00 36.99 3.69
108 109 6.629128 CACTGCTATGTCATCTATAAGGAGG 58.371 44.000 6.16 0.00 0.00 4.30
109 110 6.435591 CACTGCTATGTCATCTATAAGGAGGA 59.564 42.308 6.16 0.00 0.00 3.71
110 111 7.013220 ACTGCTATGTCATCTATAAGGAGGAA 58.987 38.462 6.16 0.00 0.00 3.36
111 112 7.178274 ACTGCTATGTCATCTATAAGGAGGAAG 59.822 40.741 6.16 0.00 0.00 3.46
112 113 6.071108 TGCTATGTCATCTATAAGGAGGAAGC 60.071 42.308 0.00 0.00 31.93 3.86
113 114 6.071108 GCTATGTCATCTATAAGGAGGAAGCA 60.071 42.308 0.00 0.00 31.74 3.91
114 115 6.753913 ATGTCATCTATAAGGAGGAAGCAA 57.246 37.500 0.00 0.00 0.00 3.91
115 116 6.166984 TGTCATCTATAAGGAGGAAGCAAG 57.833 41.667 0.00 0.00 0.00 4.01
116 117 4.994217 GTCATCTATAAGGAGGAAGCAAGC 59.006 45.833 0.00 0.00 0.00 4.01
117 118 4.655649 TCATCTATAAGGAGGAAGCAAGCA 59.344 41.667 0.00 0.00 0.00 3.91
118 119 5.130975 TCATCTATAAGGAGGAAGCAAGCAA 59.869 40.000 0.00 0.00 0.00 3.91
119 120 5.028549 TCTATAAGGAGGAAGCAAGCAAG 57.971 43.478 0.00 0.00 0.00 4.01
120 121 3.728385 ATAAGGAGGAAGCAAGCAAGT 57.272 42.857 0.00 0.00 0.00 3.16
121 122 1.902938 AAGGAGGAAGCAAGCAAGTC 58.097 50.000 0.00 0.00 0.00 3.01
122 123 1.063183 AGGAGGAAGCAAGCAAGTCT 58.937 50.000 0.00 0.00 0.00 3.24
123 124 1.423161 AGGAGGAAGCAAGCAAGTCTT 59.577 47.619 0.00 0.00 34.78 3.01
124 125 2.158549 AGGAGGAAGCAAGCAAGTCTTT 60.159 45.455 0.00 0.00 31.27 2.52
125 126 3.073062 AGGAGGAAGCAAGCAAGTCTTTA 59.927 43.478 0.00 0.00 31.27 1.85
126 127 3.189495 GGAGGAAGCAAGCAAGTCTTTAC 59.811 47.826 0.00 0.00 31.27 2.01
127 128 3.815401 GAGGAAGCAAGCAAGTCTTTACA 59.185 43.478 0.00 0.00 31.27 2.41
128 129 4.401925 AGGAAGCAAGCAAGTCTTTACAT 58.598 39.130 0.00 0.00 31.27 2.29
129 130 5.560724 AGGAAGCAAGCAAGTCTTTACATA 58.439 37.500 0.00 0.00 31.27 2.29
130 131 6.183347 AGGAAGCAAGCAAGTCTTTACATAT 58.817 36.000 0.00 0.00 31.27 1.78
131 132 7.338710 AGGAAGCAAGCAAGTCTTTACATATA 58.661 34.615 0.00 0.00 31.27 0.86
132 133 7.829211 AGGAAGCAAGCAAGTCTTTACATATAA 59.171 33.333 0.00 0.00 31.27 0.98
133 134 8.624776 GGAAGCAAGCAAGTCTTTACATATAAT 58.375 33.333 0.00 0.00 31.27 1.28
136 137 9.793252 AGCAAGCAAGTCTTTACATATAATTTG 57.207 29.630 0.00 0.00 31.27 2.32
137 138 9.787532 GCAAGCAAGTCTTTACATATAATTTGA 57.212 29.630 0.00 0.00 31.27 2.69
164 165 8.387190 AGGGTTACATAAGAAAGTAAACACAC 57.613 34.615 0.00 0.00 39.16 3.82
165 166 7.994334 AGGGTTACATAAGAAAGTAAACACACA 59.006 33.333 0.00 0.00 39.16 3.72
166 167 8.071967 GGGTTACATAAGAAAGTAAACACACAC 58.928 37.037 0.00 0.00 39.16 3.82
167 168 8.614346 GGTTACATAAGAAAGTAAACACACACA 58.386 33.333 0.00 0.00 37.73 3.72
168 169 9.429600 GTTACATAAGAAAGTAAACACACACAC 57.570 33.333 0.00 0.00 32.55 3.82
169 170 6.711579 ACATAAGAAAGTAAACACACACACG 58.288 36.000 0.00 0.00 0.00 4.49
170 171 6.535865 ACATAAGAAAGTAAACACACACACGA 59.464 34.615 0.00 0.00 0.00 4.35
171 172 5.464965 AAGAAAGTAAACACACACACGAG 57.535 39.130 0.00 0.00 0.00 4.18
172 173 4.751060 AGAAAGTAAACACACACACGAGA 58.249 39.130 0.00 0.00 0.00 4.04
179 180 2.695359 ACACACACACGAGAACAAACT 58.305 42.857 0.00 0.00 0.00 2.66
243 244 0.247460 GCAGCCCCACCTTTTCATTC 59.753 55.000 0.00 0.00 0.00 2.67
259 260 2.754552 TCATTCATTAGCCCAAGCACAC 59.245 45.455 0.00 0.00 43.56 3.82
319 320 4.351874 TTCCTCTCGTTCCAAATGTTCT 57.648 40.909 0.00 0.00 0.00 3.01
340 341 5.348164 TCTCACACGGTGTACATGATAATG 58.652 41.667 14.30 0.00 34.79 1.90
386 393 1.213926 AGATTCTTGCTCCACCATCCC 59.786 52.381 0.00 0.00 0.00 3.85
397 404 2.041620 TCCACCATCCCTCAAAAGAAGG 59.958 50.000 0.00 0.00 0.00 3.46
414 426 1.745489 GGTTCATCCTGCCGTGGTC 60.745 63.158 0.00 0.00 0.00 4.02
415 427 1.003839 GTTCATCCTGCCGTGGTCA 60.004 57.895 0.00 0.00 0.00 4.02
425 437 2.290641 CTGCCGTGGTCATAAAATAGGC 59.709 50.000 0.00 0.00 43.26 3.93
460 507 4.196193 TGCTAGCCCATATGTGTGTAAAC 58.804 43.478 13.29 0.00 0.00 2.01
463 510 5.124776 GCTAGCCCATATGTGTGTAAACAAA 59.875 40.000 2.29 0.00 32.81 2.83
466 513 5.303078 AGCCCATATGTGTGTAAACAAAACA 59.697 36.000 1.24 3.23 32.81 2.83
467 514 5.986135 GCCCATATGTGTGTAAACAAAACAA 59.014 36.000 1.24 0.00 32.81 2.83
488 590 9.979578 AAACAATATTTCACATTGCTAAGTTGA 57.020 25.926 0.00 0.00 36.96 3.18
520 622 7.765695 ACCCATGCATGGTATTTAATTAGAG 57.234 36.000 37.30 22.26 46.65 2.43
538 640 1.133407 GAGCTAGCTAGTGCGTGTCTT 59.867 52.381 19.38 0.00 45.42 3.01
539 641 1.546476 AGCTAGCTAGTGCGTGTCTTT 59.454 47.619 17.69 0.00 45.42 2.52
550 652 6.371809 AGTGCGTGTCTTTTTAAATCTCAA 57.628 33.333 0.00 0.00 0.00 3.02
569 671 4.984295 TCAATTGTCCTCCAACTCATTCA 58.016 39.130 5.13 0.00 35.44 2.57
579 681 5.106396 CCTCCAACTCATTCATGTTCTTGTC 60.106 44.000 0.00 0.00 0.00 3.18
586 688 6.652481 ACTCATTCATGTTCTTGTCTAGTTGG 59.348 38.462 0.00 0.00 0.00 3.77
598 700 8.727100 TCTTGTCTAGTTGGATATGGATATGT 57.273 34.615 0.00 0.00 0.00 2.29
665 767 3.463329 AGGTTATCACTATGTGGGGCAAT 59.537 43.478 0.00 0.00 33.87 3.56
678 780 5.022122 TGTGGGGCAATCATAAAGAATCAA 58.978 37.500 0.00 0.00 0.00 2.57
707 809 1.140452 TGCTTGCTTGCCAATTGGAAA 59.860 42.857 29.02 23.08 37.39 3.13
719 822 6.201591 TGCCAATTGGAAAAGGATAAGGTAT 58.798 36.000 29.02 0.00 37.39 2.73
768 871 2.558795 GGTTTTCCTCCTTTGCTTCCTC 59.441 50.000 0.00 0.00 36.94 3.71
770 873 2.867109 TTCCTCCTTTGCTTCCTCTG 57.133 50.000 0.00 0.00 0.00 3.35
773 876 1.163554 CTCCTTTGCTTCCTCTGTGC 58.836 55.000 0.00 0.00 0.00 4.57
787 890 4.160635 GTGCGCGTGGTATGGTGC 62.161 66.667 8.43 0.00 39.98 5.01
804 907 2.190981 GTGCGGTGTATACACTACAGC 58.809 52.381 29.89 26.90 45.73 4.40
805 908 1.819903 TGCGGTGTATACACTACAGCA 59.180 47.619 29.89 28.55 45.73 4.41
806 909 2.231721 TGCGGTGTATACACTACAGCAA 59.768 45.455 29.89 18.23 45.73 3.91
807 910 3.118920 TGCGGTGTATACACTACAGCAAT 60.119 43.478 29.89 0.00 45.73 3.56
808 911 4.098196 TGCGGTGTATACACTACAGCAATA 59.902 41.667 29.89 14.65 45.73 1.90
809 912 4.680110 GCGGTGTATACACTACAGCAATAG 59.320 45.833 29.89 12.74 45.73 1.73
810 913 5.735354 GCGGTGTATACACTACAGCAATAGT 60.735 44.000 29.89 0.00 45.73 2.12
811 914 6.270815 CGGTGTATACACTACAGCAATAGTT 58.729 40.000 29.89 0.00 45.73 2.24
812 915 6.755141 CGGTGTATACACTACAGCAATAGTTT 59.245 38.462 29.89 0.00 45.73 2.66
813 916 7.277098 CGGTGTATACACTACAGCAATAGTTTT 59.723 37.037 29.89 0.00 45.73 2.43
814 917 8.943002 GGTGTATACACTACAGCAATAGTTTTT 58.057 33.333 29.89 0.00 45.73 1.94
844 947 9.616156 TTTTGAGAAATAGTAGTGTAACAACCA 57.384 29.630 0.00 0.00 41.43 3.67
855 958 8.319146 AGTAGTGTAACAACCACTATAAATGCT 58.681 33.333 3.84 0.00 44.67 3.79
888 991 3.612479 GCCATGACAACACACCTCAATTC 60.612 47.826 0.00 0.00 0.00 2.17
943 1046 2.223923 CCACCTAGCAAGCTAGCTACAG 60.224 54.545 19.70 12.31 44.50 2.74
1015 1118 4.929707 CGATGGCCGCCCTAACCC 62.930 72.222 7.03 0.00 0.00 4.11
1071 1174 4.492160 GCGATCACCGACGAGGCA 62.492 66.667 0.00 0.00 46.52 4.75
1073 1176 2.571757 GATCACCGACGAGGCACA 59.428 61.111 0.00 0.00 46.52 4.57
1074 1177 1.080093 GATCACCGACGAGGCACAA 60.080 57.895 0.00 0.00 46.52 3.33
1128 1231 4.449131 TCATCAAGGATGAGATGAACAGC 58.551 43.478 4.86 0.00 45.42 4.40
1169 1272 3.319198 GACCAAGACGGAGGGCCA 61.319 66.667 6.18 0.00 38.63 5.36
1258 1361 1.153842 CAGCGCTACATCCACGACA 60.154 57.895 10.99 0.00 0.00 4.35
1279 1382 0.678048 GGTCCCGAATGAAGCTGCTT 60.678 55.000 15.92 15.92 0.00 3.91
1285 1388 2.483877 CCGAATGAAGCTGCTTGTTGTA 59.516 45.455 21.25 1.17 0.00 2.41
1288 1391 4.093998 CGAATGAAGCTGCTTGTTGTAGAT 59.906 41.667 21.25 0.00 0.00 1.98
1289 1392 5.557891 AATGAAGCTGCTTGTTGTAGATC 57.442 39.130 21.25 2.24 0.00 2.75
1302 1405 3.714078 TAGATCCCTGGGCGCCCTT 62.714 63.158 43.34 23.78 36.94 3.95
1338 1441 0.042731 TACTCCTCCTCCACCCCAAG 59.957 60.000 0.00 0.00 0.00 3.61
1345 1448 1.423921 TCCTCCACCCCAAGAAGTTTC 59.576 52.381 0.00 0.00 0.00 2.78
1355 1458 0.391597 AAGAAGTTTCGTCGGCTCCA 59.608 50.000 0.00 0.00 0.00 3.86
1475 1584 5.452302 CGTAAGTGAAGCAAACTTTCACTTG 59.548 40.000 29.36 17.51 44.61 3.16
1765 2092 4.037684 GCCTCCTATGAAAGACTTACGCTA 59.962 45.833 0.00 0.00 0.00 4.26
1905 2243 2.747855 CGCCCTGCTCCAAAGTCC 60.748 66.667 0.00 0.00 0.00 3.85
1957 2303 0.035820 ATGGCTAACCCGAGCGAAAA 60.036 50.000 0.00 0.00 43.83 2.29
2072 2422 3.820467 TGCAAATCAAAGATCGGAAGTGT 59.180 39.130 0.00 0.00 0.00 3.55
2202 2570 1.557443 CTGTGCGGTCGACCAACTTC 61.557 60.000 32.80 19.75 35.14 3.01
2203 2571 1.593209 GTGCGGTCGACCAACTTCA 60.593 57.895 32.80 18.41 35.14 3.02
2217 2585 3.308688 CCAACTTCACCTCCCTCATCAAT 60.309 47.826 0.00 0.00 0.00 2.57
2290 2658 0.611714 AAAGCACACTAGTACGGGGG 59.388 55.000 0.00 0.00 0.00 5.40
2324 2692 7.916914 AAACGTGGTTCTGCTTTATATTAGT 57.083 32.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.057316 GCATGCATACGTCAGAGCTAG 58.943 52.381 14.21 0.00 0.00 3.42
1 2 1.600413 CGCATGCATACGTCAGAGCTA 60.600 52.381 19.57 0.00 0.00 3.32
2 3 0.873312 CGCATGCATACGTCAGAGCT 60.873 55.000 19.57 0.00 0.00 4.09
3 4 1.148157 ACGCATGCATACGTCAGAGC 61.148 55.000 19.10 5.24 38.28 4.09
4 5 0.573987 CACGCATGCATACGTCAGAG 59.426 55.000 21.77 7.51 41.32 3.35
5 6 2.664567 CACGCATGCATACGTCAGA 58.335 52.632 21.77 0.00 41.32 3.27
16 17 2.182284 CCCACAATGGCACGCATG 59.818 61.111 0.00 0.00 35.79 4.06
28 29 2.230025 CGGACATTAATTTGTGCCCACA 59.770 45.455 0.00 0.00 39.98 4.17
29 30 2.490115 TCGGACATTAATTTGTGCCCAC 59.510 45.455 0.00 0.00 34.77 4.61
30 31 2.490115 GTCGGACATTAATTTGTGCCCA 59.510 45.455 2.62 0.00 34.77 5.36
31 32 2.752903 AGTCGGACATTAATTTGTGCCC 59.247 45.455 11.27 0.00 34.77 5.36
32 33 3.181500 GGAGTCGGACATTAATTTGTGCC 60.181 47.826 11.27 0.00 34.77 5.01
33 34 3.689649 AGGAGTCGGACATTAATTTGTGC 59.310 43.478 11.27 0.00 34.90 4.57
34 35 5.880054 AAGGAGTCGGACATTAATTTGTG 57.120 39.130 11.27 0.00 0.00 3.33
35 36 6.894339 AAAAGGAGTCGGACATTAATTTGT 57.106 33.333 11.27 0.00 0.00 2.83
66 67 5.186996 CAGTGCTCCTGCTTCTTTAAAAA 57.813 39.130 0.00 0.00 40.48 1.94
67 68 4.836125 CAGTGCTCCTGCTTCTTTAAAA 57.164 40.909 0.00 0.00 40.48 1.52
78 79 2.102757 AGATGACATAGCAGTGCTCCTG 59.897 50.000 23.64 21.64 44.53 3.86
79 80 2.396608 AGATGACATAGCAGTGCTCCT 58.603 47.619 23.64 7.69 40.44 3.69
80 81 2.906691 AGATGACATAGCAGTGCTCC 57.093 50.000 23.64 10.13 40.44 4.70
81 82 6.071672 TCCTTATAGATGACATAGCAGTGCTC 60.072 42.308 23.64 8.13 40.44 4.26
82 83 5.777223 TCCTTATAGATGACATAGCAGTGCT 59.223 40.000 23.44 23.44 43.41 4.40
83 84 6.030548 TCCTTATAGATGACATAGCAGTGC 57.969 41.667 7.13 7.13 0.00 4.40
84 85 6.435591 TCCTCCTTATAGATGACATAGCAGTG 59.564 42.308 0.00 0.00 0.00 3.66
85 86 6.556639 TCCTCCTTATAGATGACATAGCAGT 58.443 40.000 0.00 0.00 0.00 4.40
86 87 7.473735 TTCCTCCTTATAGATGACATAGCAG 57.526 40.000 0.00 0.00 0.00 4.24
87 88 6.071108 GCTTCCTCCTTATAGATGACATAGCA 60.071 42.308 0.00 0.00 0.00 3.49
88 89 6.071108 TGCTTCCTCCTTATAGATGACATAGC 60.071 42.308 0.00 0.00 0.00 2.97
89 90 7.473735 TGCTTCCTCCTTATAGATGACATAG 57.526 40.000 0.00 0.00 0.00 2.23
90 91 7.526192 GCTTGCTTCCTCCTTATAGATGACATA 60.526 40.741 0.00 0.00 0.00 2.29
91 92 6.743773 GCTTGCTTCCTCCTTATAGATGACAT 60.744 42.308 0.00 0.00 0.00 3.06
92 93 5.453903 GCTTGCTTCCTCCTTATAGATGACA 60.454 44.000 0.00 0.00 0.00 3.58
93 94 4.994217 GCTTGCTTCCTCCTTATAGATGAC 59.006 45.833 0.00 0.00 0.00 3.06
94 95 4.655649 TGCTTGCTTCCTCCTTATAGATGA 59.344 41.667 0.00 0.00 0.00 2.92
95 96 4.965814 TGCTTGCTTCCTCCTTATAGATG 58.034 43.478 0.00 0.00 0.00 2.90
96 97 5.131809 ACTTGCTTGCTTCCTCCTTATAGAT 59.868 40.000 0.00 0.00 0.00 1.98
97 98 4.471386 ACTTGCTTGCTTCCTCCTTATAGA 59.529 41.667 0.00 0.00 0.00 1.98
98 99 4.775236 ACTTGCTTGCTTCCTCCTTATAG 58.225 43.478 0.00 0.00 0.00 1.31
99 100 4.471386 AGACTTGCTTGCTTCCTCCTTATA 59.529 41.667 0.00 0.00 0.00 0.98
100 101 3.265479 AGACTTGCTTGCTTCCTCCTTAT 59.735 43.478 0.00 0.00 0.00 1.73
101 102 2.639839 AGACTTGCTTGCTTCCTCCTTA 59.360 45.455 0.00 0.00 0.00 2.69
102 103 1.423161 AGACTTGCTTGCTTCCTCCTT 59.577 47.619 0.00 0.00 0.00 3.36
103 104 1.063183 AGACTTGCTTGCTTCCTCCT 58.937 50.000 0.00 0.00 0.00 3.69
104 105 1.902938 AAGACTTGCTTGCTTCCTCC 58.097 50.000 0.00 0.00 34.93 4.30
105 106 3.815401 TGTAAAGACTTGCTTGCTTCCTC 59.185 43.478 0.00 0.00 36.80 3.71
106 107 3.820557 TGTAAAGACTTGCTTGCTTCCT 58.179 40.909 0.00 0.00 36.80 3.36
107 108 4.773323 ATGTAAAGACTTGCTTGCTTCC 57.227 40.909 0.00 0.00 36.80 3.46
110 111 9.793252 CAAATTATATGTAAAGACTTGCTTGCT 57.207 29.630 0.00 0.00 36.80 3.91
111 112 9.787532 TCAAATTATATGTAAAGACTTGCTTGC 57.212 29.630 0.00 0.00 36.80 4.01
138 139 9.492973 GTGTGTTTACTTTCTTATGTAACCCTA 57.507 33.333 0.00 0.00 0.00 3.53
139 140 7.994334 TGTGTGTTTACTTTCTTATGTAACCCT 59.006 33.333 0.00 0.00 0.00 4.34
140 141 8.071967 GTGTGTGTTTACTTTCTTATGTAACCC 58.928 37.037 0.00 0.00 0.00 4.11
141 142 8.614346 TGTGTGTGTTTACTTTCTTATGTAACC 58.386 33.333 0.00 0.00 0.00 2.85
142 143 9.429600 GTGTGTGTGTTTACTTTCTTATGTAAC 57.570 33.333 0.00 0.00 0.00 2.50
143 144 8.329583 CGTGTGTGTGTTTACTTTCTTATGTAA 58.670 33.333 0.00 0.00 0.00 2.41
144 145 7.705752 TCGTGTGTGTGTTTACTTTCTTATGTA 59.294 33.333 0.00 0.00 0.00 2.29
145 146 6.535865 TCGTGTGTGTGTTTACTTTCTTATGT 59.464 34.615 0.00 0.00 0.00 2.29
146 147 6.939627 TCGTGTGTGTGTTTACTTTCTTATG 58.060 36.000 0.00 0.00 0.00 1.90
147 148 6.982141 TCTCGTGTGTGTGTTTACTTTCTTAT 59.018 34.615 0.00 0.00 0.00 1.73
148 149 6.331845 TCTCGTGTGTGTGTTTACTTTCTTA 58.668 36.000 0.00 0.00 0.00 2.10
149 150 5.172934 TCTCGTGTGTGTGTTTACTTTCTT 58.827 37.500 0.00 0.00 0.00 2.52
150 151 4.751060 TCTCGTGTGTGTGTTTACTTTCT 58.249 39.130 0.00 0.00 0.00 2.52
151 152 5.163933 TGTTCTCGTGTGTGTGTTTACTTTC 60.164 40.000 0.00 0.00 0.00 2.62
152 153 4.691685 TGTTCTCGTGTGTGTGTTTACTTT 59.308 37.500 0.00 0.00 0.00 2.66
153 154 4.247258 TGTTCTCGTGTGTGTGTTTACTT 58.753 39.130 0.00 0.00 0.00 2.24
154 155 3.852286 TGTTCTCGTGTGTGTGTTTACT 58.148 40.909 0.00 0.00 0.00 2.24
155 156 4.587211 TTGTTCTCGTGTGTGTGTTTAC 57.413 40.909 0.00 0.00 0.00 2.01
156 157 4.691685 AGTTTGTTCTCGTGTGTGTGTTTA 59.308 37.500 0.00 0.00 0.00 2.01
157 158 3.500680 AGTTTGTTCTCGTGTGTGTGTTT 59.499 39.130 0.00 0.00 0.00 2.83
158 159 3.071479 AGTTTGTTCTCGTGTGTGTGTT 58.929 40.909 0.00 0.00 0.00 3.32
159 160 2.695359 AGTTTGTTCTCGTGTGTGTGT 58.305 42.857 0.00 0.00 0.00 3.72
160 161 3.740044 AAGTTTGTTCTCGTGTGTGTG 57.260 42.857 0.00 0.00 0.00 3.82
161 162 5.866335 TTTAAGTTTGTTCTCGTGTGTGT 57.134 34.783 0.00 0.00 0.00 3.72
219 220 2.779742 AAAAGGTGGGGCTGCGCATA 62.780 55.000 12.24 3.97 0.00 3.14
243 244 1.137404 GCGTGTGCTTGGGCTAATG 59.863 57.895 0.00 0.00 39.59 1.90
259 260 6.498304 AGCATAAATCATTTCTAACTTGGCG 58.502 36.000 0.00 0.00 0.00 5.69
319 320 4.438148 CCATTATCATGTACACCGTGTGA 58.562 43.478 14.66 3.28 36.96 3.58
340 341 2.338785 GGTGCTCTCTTTGGCTGCC 61.339 63.158 12.87 12.87 0.00 4.85
397 404 0.392998 ATGACCACGGCAGGATGAAC 60.393 55.000 0.00 0.00 39.69 3.18
406 418 2.294074 TGCCTATTTTATGACCACGGC 58.706 47.619 0.00 0.00 36.85 5.68
408 420 3.945285 AGGTTGCCTATTTTATGACCACG 59.055 43.478 0.00 0.00 28.47 4.94
414 426 7.651808 CATTGGACTAGGTTGCCTATTTTATG 58.348 38.462 0.00 0.00 35.36 1.90
415 427 6.265422 GCATTGGACTAGGTTGCCTATTTTAT 59.735 38.462 0.00 0.00 35.36 1.40
425 437 2.565841 GGCTAGCATTGGACTAGGTTG 58.434 52.381 18.24 0.00 38.05 3.77
467 514 8.844244 GGAGATCAACTTAGCAATGTGAAATAT 58.156 33.333 0.00 0.00 0.00 1.28
473 575 5.885230 TTGGAGATCAACTTAGCAATGTG 57.115 39.130 0.00 0.00 0.00 3.21
484 586 2.170166 TGCATGGGTTTGGAGATCAAC 58.830 47.619 0.00 0.00 34.67 3.18
486 588 2.380941 CATGCATGGGTTTGGAGATCA 58.619 47.619 19.40 0.00 0.00 2.92
488 590 1.784358 CCATGCATGGGTTTGGAGAT 58.216 50.000 34.31 0.00 44.31 2.75
520 622 1.997669 AAAGACACGCACTAGCTAGC 58.002 50.000 20.91 6.62 39.10 3.42
529 631 7.199766 ACAATTGAGATTTAAAAAGACACGCA 58.800 30.769 13.59 0.00 0.00 5.24
538 640 8.477419 AGTTGGAGGACAATTGAGATTTAAAA 57.523 30.769 13.59 0.00 41.95 1.52
539 641 7.723616 TGAGTTGGAGGACAATTGAGATTTAAA 59.276 33.333 13.59 0.00 41.95 1.52
550 652 4.927049 ACATGAATGAGTTGGAGGACAAT 58.073 39.130 0.00 0.00 41.95 2.71
569 671 7.437713 TCCATATCCAACTAGACAAGAACAT 57.562 36.000 0.00 0.00 0.00 2.71
640 742 3.883489 GCCCCACATAGTGATAACCTTTC 59.117 47.826 0.00 0.00 35.23 2.62
643 745 2.487775 TGCCCCACATAGTGATAACCT 58.512 47.619 0.00 0.00 35.23 3.50
651 753 5.387113 TCTTTATGATTGCCCCACATAGT 57.613 39.130 0.00 0.00 0.00 2.12
652 754 6.491062 TGATTCTTTATGATTGCCCCACATAG 59.509 38.462 0.00 0.00 0.00 2.23
654 756 5.210430 TGATTCTTTATGATTGCCCCACAT 58.790 37.500 0.00 0.00 0.00 3.21
665 767 8.158169 AGCAATAGCGAATTGATTCTTTATGA 57.842 30.769 16.21 0.00 46.81 2.15
719 822 4.500887 CGGAGGGCAAAGAGTCGAATATTA 60.501 45.833 0.00 0.00 0.00 0.98
768 871 2.434185 ACCATACCACGCGCACAG 60.434 61.111 5.73 0.00 0.00 3.66
770 873 4.160635 GCACCATACCACGCGCAC 62.161 66.667 5.73 0.00 0.00 5.34
818 921 9.616156 TGGTTGTTACACTACTATTTCTCAAAA 57.384 29.630 0.00 0.00 0.00 2.44
819 922 9.048446 GTGGTTGTTACACTACTATTTCTCAAA 57.952 33.333 0.00 0.00 35.98 2.69
820 923 8.426489 AGTGGTTGTTACACTACTATTTCTCAA 58.574 33.333 0.00 0.00 46.62 3.02
821 924 7.959175 AGTGGTTGTTACACTACTATTTCTCA 58.041 34.615 0.00 0.00 46.62 3.27
842 945 1.532868 GCGAGGCAGCATTTATAGTGG 59.467 52.381 0.00 0.00 37.05 4.00
843 946 1.532868 GGCGAGGCAGCATTTATAGTG 59.467 52.381 7.25 0.00 39.27 2.74
844 947 1.543429 GGGCGAGGCAGCATTTATAGT 60.543 52.381 7.25 0.00 39.27 2.12
888 991 1.349259 GCCTTGCTCTTTTGCATGCG 61.349 55.000 14.09 0.00 42.96 4.73
904 1007 1.456705 GATCGAGAGGGAGGTGCCT 60.457 63.158 0.00 0.00 36.66 4.75
1015 1118 3.814268 CCCGTCAATGGCGCCTTG 61.814 66.667 29.70 26.34 0.00 3.61
1071 1174 4.373116 ACGCCGCCGATCAGTTGT 62.373 61.111 0.00 0.00 38.29 3.32
1073 1176 4.814294 GGACGCCGCCGATCAGTT 62.814 66.667 0.00 0.00 38.29 3.16
1128 1231 0.458669 GCAGCAGGAACCCATTCATG 59.541 55.000 0.00 0.00 46.96 3.07
1169 1272 3.681835 GGACCTGGTCGTCGTGCT 61.682 66.667 19.98 0.00 33.30 4.40
1258 1361 0.749454 GCAGCTTCATTCGGGACCAT 60.749 55.000 0.00 0.00 0.00 3.55
1267 1370 4.397417 GGATCTACAACAAGCAGCTTCATT 59.603 41.667 4.07 0.00 0.00 2.57
1279 1382 1.904771 CGCCCAGGGATCTACAACA 59.095 57.895 10.89 0.00 0.00 3.33
1320 1423 1.229658 CTTGGGGTGGAGGAGGAGT 60.230 63.158 0.00 0.00 0.00 3.85
1338 1441 0.599204 TGTGGAGCCGACGAAACTTC 60.599 55.000 0.00 0.00 0.00 3.01
1345 1448 4.742201 CCCTGTGTGGAGCCGACG 62.742 72.222 0.00 0.00 38.35 5.12
1355 1458 3.314331 CTGGAGACGGCCCTGTGT 61.314 66.667 0.00 0.00 0.00 3.72
1765 2092 4.572571 TCCCTTGCCGCCGTTGTT 62.573 61.111 0.00 0.00 0.00 2.83
1823 2155 2.125147 GTGTATGCTGCTGCCGGA 60.125 61.111 5.05 0.00 38.71 5.14
1900 2238 3.169908 GAGGAGAAAGAGGTCTGGACTT 58.830 50.000 0.67 0.00 0.00 3.01
1905 2243 6.154363 ACTTAGATTGAGGAGAAAGAGGTCTG 59.846 42.308 0.00 0.00 0.00 3.51
1957 2303 2.288457 CCGATCCAATCTCACGTAGCAT 60.288 50.000 0.00 0.00 0.00 3.79
2072 2422 2.124320 GCCGGCAGCCCATTCTAA 60.124 61.111 24.80 0.00 34.35 2.10
2194 2562 1.630878 GATGAGGGAGGTGAAGTTGGT 59.369 52.381 0.00 0.00 0.00 3.67
2217 2585 1.839747 AACCACGTAGTCAGCCCCA 60.840 57.895 0.00 0.00 41.61 4.96
2290 2658 0.939419 AACCACGTTTAACCAGTCGC 59.061 50.000 0.00 0.00 0.00 5.19
2324 2692 2.010582 GCCAGTTCCGGTTGTGCAAA 62.011 55.000 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.