Multiple sequence alignment - TraesCS5D01G206800

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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 TraesCS5D01G206800 chr5D 100.000 3414 0 0 1 3414 313152880 313149467 0.000000e+00 6305.0
1 TraesCS5D01G206800 chr5D 86.719 1137 81 29 1 1123 313332099 313333179 0.000000e+00 1199.0
2 TraesCS5D01G206800 chr5D 87.266 1013 117 8 1225 2232 313333239 313334244 0.000000e+00 1146.0
3 TraesCS5D01G206800 chr5D 90.232 604 54 4 1748 2347 313284300 313284902 0.000000e+00 784.0
4 TraesCS5D01G206800 chr5D 82.927 410 41 16 2235 2637 313343842 313344229 3.260000e-90 342.0
5 TraesCS5D01G206800 chr5D 90.071 141 9 4 2705 2845 313144502 313144367 9.740000e-41 178.0
6 TraesCS5D01G206800 chr5D 81.250 224 39 3 2844 3065 561996084 561996306 9.740000e-41 178.0
7 TraesCS5D01G206800 chr5D 87.943 141 10 3 2346 2483 313328082 313328218 3.530000e-35 159.0
8 TraesCS5D01G206800 chr5B 93.458 1070 59 7 2346 3414 360859962 360858903 0.000000e+00 1578.0
9 TraesCS5D01G206800 chr5B 91.439 1133 91 5 1222 2351 360861134 360860005 0.000000e+00 1550.0
10 TraesCS5D01G206800 chr5B 92.108 925 56 11 1 916 360862281 360861365 0.000000e+00 1288.0
11 TraesCS5D01G206800 chr5B 86.722 964 117 6 1386 2347 360925005 360925959 0.000000e+00 1061.0
12 TraesCS5D01G206800 chr5B 90.909 297 25 1 1 297 360922283 360922577 6.860000e-107 398.0
13 TraesCS5D01G206800 chr5B 80.340 529 61 20 2355 2850 360926020 360926538 9.010000e-96 361.0
14 TraesCS5D01G206800 chr5A 95.098 918 37 4 1 918 407126232 407125323 0.000000e+00 1439.0
15 TraesCS5D01G206800 chr5A 88.448 1108 119 7 1248 2347 407125095 407123989 0.000000e+00 1328.0
16 TraesCS5D01G206800 chr5A 90.817 893 71 7 1 882 407153657 407154549 0.000000e+00 1184.0
17 TraesCS5D01G206800 chr5A 84.518 1182 139 17 1183 2347 407156605 407157759 0.000000e+00 1129.0
18 TraesCS5D01G206800 chr5A 81.546 401 46 14 2473 2850 407158266 407158661 4.280000e-79 305.0
19 TraesCS5D01G206800 chr5A 91.935 62 1 1 2428 2489 407158193 407158250 2.180000e-12 84.2
20 TraesCS5D01G206800 chr4A 83.283 329 45 9 2844 3171 545110117 545110436 9.260000e-76 294.0
21 TraesCS5D01G206800 chr4A 82.569 218 32 5 2866 3081 3071412 3071199 1.620000e-43 187.0
22 TraesCS5D01G206800 chr7A 81.712 257 40 4 1267 1521 581040247 581039996 1.240000e-49 207.0
23 TraesCS5D01G206800 chr7A 81.933 238 40 3 2847 3083 708600063 708599828 7.470000e-47 198.0
24 TraesCS5D01G206800 chr1B 83.117 231 35 4 2847 3076 4065165 4064938 1.240000e-49 207.0
25 TraesCS5D01G206800 chr7D 81.328 241 40 4 2842 3081 600889101 600888865 1.250000e-44 191.0
26 TraesCS5D01G206800 chr6A 84.737 190 27 2 2832 3019 583283346 583283535 4.500000e-44 189.0
27 TraesCS5D01G206800 chr3B 80.579 242 43 4 2852 3091 38457315 38457076 2.090000e-42 183.0
28 TraesCS5D01G206800 chr7B 85.950 121 17 0 1267 1387 538574995 538574875 2.760000e-26 130.0


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 TraesCS5D01G206800 chr5D 313149467 313152880 3413 True 6305.000000 6305 100.000000 1 3414 1 chr5D.!!$R2 3413
1 TraesCS5D01G206800 chr5D 313328082 313334244 6162 False 834.666667 1199 87.309333 1 2483 3 chr5D.!!$F4 2482
2 TraesCS5D01G206800 chr5D 313284300 313284902 602 False 784.000000 784 90.232000 1748 2347 1 chr5D.!!$F1 599
3 TraesCS5D01G206800 chr5B 360858903 360862281 3378 True 1472.000000 1578 92.335000 1 3414 3 chr5B.!!$R1 3413
4 TraesCS5D01G206800 chr5B 360922283 360926538 4255 False 606.666667 1061 85.990333 1 2850 3 chr5B.!!$F1 2849
5 TraesCS5D01G206800 chr5A 407123989 407126232 2243 True 1383.500000 1439 91.773000 1 2347 2 chr5A.!!$R1 2346
6 TraesCS5D01G206800 chr5A 407153657 407158661 5004 False 675.550000 1184 87.204000 1 2850 4 chr5A.!!$F1 2849

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
527 4556 0.323451 TGAGCGAGAGAAGGCACCTA 60.323 55.0 0.00 0.0 0.00 3.08 F
1243 7159 0.322277 TGCGGTTAGAGGAGAGACGT 60.322 55.0 0.00 0.0 0.00 4.34 F
1774 9949 0.105408 AAGTTTACGGCGTCACCAGT 59.895 50.0 19.21 0.0 39.03 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 9815 0.027979 CAACCATCTTGCGCATACCG 59.972 55.0 12.75 0.0 40.75 4.02 R
2216 10396 0.247185 CGCCATTGCCAACCTTCATT 59.753 50.0 0.00 0.0 0.00 2.57 R
2913 11559 0.755327 GTTGGGGGTGCAAGTTGTCT 60.755 55.0 4.48 0.0 0.00 3.41 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
42 4060 2.003301 CTTTTCTTAGACCGAGCTGGC 58.997 52.381 0.00 0.00 43.94 4.85
62 4080 3.017323 GCATGGAACGATGCTCCG 58.983 61.111 13.00 0.00 44.57 4.63
298 4316 3.649986 GCCGCGTGTGCTGAACTT 61.650 61.111 4.92 0.00 39.65 2.66
317 4335 3.009143 ACTTTGGGTATGGTGAGAACTCC 59.991 47.826 0.00 0.00 0.00 3.85
322 4340 2.622436 GTATGGTGAGAACTCCAGTGC 58.378 52.381 0.00 0.00 41.88 4.40
339 4357 3.183574 CAGTGCGACAATCTGACGTTTAA 59.816 43.478 0.00 0.00 37.80 1.52
527 4556 0.323451 TGAGCGAGAGAAGGCACCTA 60.323 55.000 0.00 0.00 0.00 3.08
737 4781 5.190528 AGGGATGCTATACAGGAATATGGTG 59.809 44.000 0.00 0.00 0.00 4.17
741 4785 4.587262 TGCTATACAGGAATATGGTGTCGT 59.413 41.667 0.00 0.00 0.00 4.34
742 4786 5.162075 GCTATACAGGAATATGGTGTCGTC 58.838 45.833 0.00 0.00 0.00 4.20
743 4787 2.579207 ACAGGAATATGGTGTCGTCG 57.421 50.000 0.00 0.00 0.00 5.12
744 4788 1.822990 ACAGGAATATGGTGTCGTCGT 59.177 47.619 0.00 0.00 0.00 4.34
745 4789 2.159282 ACAGGAATATGGTGTCGTCGTC 60.159 50.000 0.00 0.00 0.00 4.20
746 4790 1.065102 AGGAATATGGTGTCGTCGTCG 59.935 52.381 0.00 0.00 38.55 5.12
747 4791 0.844503 GAATATGGTGTCGTCGTCGC 59.155 55.000 0.00 0.00 36.96 5.19
748 4792 0.454600 AATATGGTGTCGTCGTCGCT 59.545 50.000 0.00 0.00 36.96 4.93
749 4793 0.454600 ATATGGTGTCGTCGTCGCTT 59.545 50.000 0.00 0.00 36.96 4.68
750 4794 0.455464 TATGGTGTCGTCGTCGCTTG 60.455 55.000 0.00 0.00 36.96 4.01
751 4795 3.764049 GGTGTCGTCGTCGCTTGC 61.764 66.667 0.00 0.00 36.96 4.01
752 4796 3.764049 GTGTCGTCGTCGCTTGCC 61.764 66.667 0.00 0.00 36.96 4.52
753 4797 3.973516 TGTCGTCGTCGCTTGCCT 61.974 61.111 0.00 0.00 36.96 4.75
754 4798 3.173240 GTCGTCGTCGCTTGCCTC 61.173 66.667 0.00 0.00 36.96 4.70
755 4799 4.753877 TCGTCGTCGCTTGCCTCG 62.754 66.667 0.00 0.00 36.96 4.63
870 4914 2.049985 AGCGCGTATCCATCTCGC 60.050 61.111 8.43 0.00 45.34 5.03
877 4921 1.527611 TATCCATCTCGCCGTCCGT 60.528 57.895 0.00 0.00 38.35 4.69
878 4922 1.512996 TATCCATCTCGCCGTCCGTC 61.513 60.000 0.00 0.00 38.35 4.79
879 4923 4.907034 CCATCTCGCCGTCCGTCG 62.907 72.222 0.00 0.00 38.35 5.12
880 4924 4.175489 CATCTCGCCGTCCGTCGT 62.175 66.667 0.00 0.00 38.35 4.34
881 4925 3.873883 ATCTCGCCGTCCGTCGTC 61.874 66.667 0.00 0.00 38.35 4.20
889 4933 2.794166 GTCCGTCGTCACGTCGTG 60.794 66.667 19.38 19.38 45.17 4.35
920 5064 4.174411 AGTTTTCTTAATTTCCTGCGCC 57.826 40.909 4.18 0.00 0.00 6.53
921 5065 3.056821 AGTTTTCTTAATTTCCTGCGCCC 60.057 43.478 4.18 0.00 0.00 6.13
924 5068 2.733956 TCTTAATTTCCTGCGCCCAAT 58.266 42.857 4.18 0.00 0.00 3.16
926 5070 2.435372 TAATTTCCTGCGCCCAATCT 57.565 45.000 4.18 0.00 0.00 2.40
927 5071 2.435372 AATTTCCTGCGCCCAATCTA 57.565 45.000 4.18 0.00 0.00 1.98
937 5081 1.731720 GCCCAATCTATGCGAGATCC 58.268 55.000 1.68 0.00 44.68 3.36
938 5082 2.001812 CCCAATCTATGCGAGATCCG 57.998 55.000 1.68 0.00 44.68 4.18
941 5085 3.502920 CCAATCTATGCGAGATCCGTAC 58.497 50.000 1.68 0.00 44.68 3.67
942 5086 3.502920 CAATCTATGCGAGATCCGTACC 58.497 50.000 1.68 0.00 44.68 3.34
945 5089 3.220110 TCTATGCGAGATCCGTACCTTT 58.780 45.455 5.66 0.00 41.15 3.11
947 5091 0.458669 TGCGAGATCCGTACCTTTCC 59.541 55.000 5.66 0.00 41.15 3.13
949 5093 1.400737 CGAGATCCGTACCTTTCCCT 58.599 55.000 0.00 0.00 0.00 4.20
950 5094 1.755380 CGAGATCCGTACCTTTCCCTT 59.245 52.381 0.00 0.00 0.00 3.95
951 5095 2.223758 CGAGATCCGTACCTTTCCCTTC 60.224 54.545 0.00 0.00 0.00 3.46
952 5096 3.032459 GAGATCCGTACCTTTCCCTTCT 58.968 50.000 0.00 0.00 0.00 2.85
955 5099 5.217400 AGATCCGTACCTTTCCCTTCTATT 58.783 41.667 0.00 0.00 0.00 1.73
956 5100 5.666265 AGATCCGTACCTTTCCCTTCTATTT 59.334 40.000 0.00 0.00 0.00 1.40
957 5101 5.767277 TCCGTACCTTTCCCTTCTATTTT 57.233 39.130 0.00 0.00 0.00 1.82
958 5102 6.872585 TCCGTACCTTTCCCTTCTATTTTA 57.127 37.500 0.00 0.00 0.00 1.52
960 5104 7.277396 TCCGTACCTTTCCCTTCTATTTTATG 58.723 38.462 0.00 0.00 0.00 1.90
1028 6875 1.074872 CGGACGCGAGGTTTAGGTTC 61.075 60.000 15.93 0.00 0.00 3.62
1056 6908 1.668751 GACCGGGATTGTACGTACGTA 59.331 52.381 23.60 23.60 0.00 3.57
1099 6957 3.519510 ACTCGGGATGGAATTCTTCTTGA 59.480 43.478 5.23 4.96 0.00 3.02
1100 6958 4.019321 ACTCGGGATGGAATTCTTCTTGAA 60.019 41.667 5.23 0.00 39.24 2.69
1122 6980 6.998074 TGAACTCCAAGAGAGAAATTTTAGCA 59.002 34.615 0.00 0.00 46.50 3.49
1147 7032 2.429907 CGATCGAGATCCAGCCGC 60.430 66.667 10.26 0.00 34.40 6.53
1148 7033 2.730733 GATCGAGATCCAGCCGCA 59.269 61.111 1.77 0.00 31.76 5.69
1149 7034 1.663074 GATCGAGATCCAGCCGCAC 60.663 63.158 1.77 0.00 31.76 5.34
1150 7035 3.490793 ATCGAGATCCAGCCGCACG 62.491 63.158 0.00 0.00 0.00 5.34
1151 7036 4.498520 CGAGATCCAGCCGCACGT 62.499 66.667 0.00 0.00 0.00 4.49
1152 7037 2.805546 GAGATCCAGCCGCACGTA 59.194 61.111 0.00 0.00 0.00 3.57
1153 7038 1.589196 GAGATCCAGCCGCACGTAC 60.589 63.158 0.00 0.00 0.00 3.67
1154 7039 2.954868 GATCCAGCCGCACGTACG 60.955 66.667 15.01 15.01 0.00 3.67
1178 7063 9.925865 ACGCGTTATTTATTTATTTTTGAAACG 57.074 25.926 5.58 0.00 39.04 3.60
1204 7119 2.111756 CGTACGCGTTATTACCACCTC 58.888 52.381 20.78 0.00 0.00 3.85
1205 7120 2.111756 GTACGCGTTATTACCACCTCG 58.888 52.381 20.78 0.00 0.00 4.63
1216 7131 3.991051 CACCTCGGTGCACGGACT 61.991 66.667 21.83 8.29 44.45 3.85
1217 7132 3.681835 ACCTCGGTGCACGGACTC 61.682 66.667 21.83 1.36 44.45 3.36
1218 7133 4.778415 CCTCGGTGCACGGACTCG 62.778 72.222 21.83 13.91 44.45 4.18
1223 7138 4.059459 GTGCACGGACTCGCGTTG 62.059 66.667 5.77 2.81 40.63 4.10
1224 7139 4.578898 TGCACGGACTCGCGTTGT 62.579 61.111 5.77 6.61 40.63 3.32
1225 7140 4.059459 GCACGGACTCGCGTTGTG 62.059 66.667 5.77 10.01 40.63 3.33
1226 7141 4.059459 CACGGACTCGCGTTGTGC 62.059 66.667 5.77 11.06 40.63 4.57
1235 7150 3.165498 GCGTTGTGCGGTTAGAGG 58.835 61.111 0.00 0.00 41.69 3.69
1241 7156 1.174783 TGTGCGGTTAGAGGAGAGAC 58.825 55.000 0.00 0.00 0.00 3.36
1243 7159 0.322277 TGCGGTTAGAGGAGAGACGT 60.322 55.000 0.00 0.00 0.00 4.34
1244 7160 0.377905 GCGGTTAGAGGAGAGACGTC 59.622 60.000 7.70 7.70 0.00 4.34
1304 7227 2.301583 GGACCTGCTTATCCTGATCCTC 59.698 54.545 0.00 0.00 0.00 3.71
1307 7230 3.135530 ACCTGCTTATCCTGATCCTCAAC 59.864 47.826 0.00 0.00 0.00 3.18
1313 7236 1.475403 TCCTGATCCTCAACCGTCTC 58.525 55.000 0.00 0.00 0.00 3.36
1480 9652 6.055588 ACTTCCAGAAAAACTTCGAGATTGA 58.944 36.000 0.00 0.00 0.00 2.57
1487 9659 1.965083 ACTTCGAGATTGACGACACG 58.035 50.000 0.00 0.00 39.46 4.49
1522 9694 1.798735 CCAAGATCTGTTGCGCCAG 59.201 57.895 4.18 6.07 0.00 4.85
1535 9707 2.813908 GCCAGCGGAAGGTACGTG 60.814 66.667 0.00 0.00 41.81 4.49
1548 9720 1.593006 GGTACGTGACACTATGCATGC 59.407 52.381 11.82 11.82 0.00 4.06
1575 9747 5.564550 AGCAGATACTCAATGTTGACCTTT 58.435 37.500 0.00 0.00 32.90 3.11
1579 9751 7.524912 CAGATACTCAATGTTGACCTTTTGAG 58.475 38.462 9.34 9.34 46.63 3.02
1581 9753 4.210331 ACTCAATGTTGACCTTTTGAGCT 58.790 39.130 10.53 0.00 45.66 4.09
1587 9759 3.128349 GTTGACCTTTTGAGCTACGACA 58.872 45.455 0.00 0.00 0.00 4.35
1588 9760 3.462483 TGACCTTTTGAGCTACGACAA 57.538 42.857 0.00 0.00 0.00 3.18
1590 9762 2.132762 ACCTTTTGAGCTACGACAACG 58.867 47.619 0.00 0.00 45.75 4.10
1593 9765 2.787601 TTTGAGCTACGACAACGACT 57.212 45.000 0.00 0.00 42.66 4.18
1598 9770 3.063588 TGAGCTACGACAACGACTATCTG 59.936 47.826 0.00 0.00 42.66 2.90
1603 9775 1.135373 CGACAACGACTATCTGCCACT 60.135 52.381 0.00 0.00 42.66 4.00
1607 9779 3.699538 ACAACGACTATCTGCCACTGATA 59.300 43.478 0.00 0.00 0.00 2.15
1625 9797 5.011090 TGATATCTCAGTTCCGGTTTGAG 57.989 43.478 19.60 19.60 39.69 3.02
1656 9831 1.821241 CGACGGTATGCGCAAGATGG 61.821 60.000 17.11 5.67 43.02 3.51
1658 9833 0.392461 ACGGTATGCGCAAGATGGTT 60.392 50.000 17.11 0.00 43.02 3.67
1671 9846 0.171007 GATGGTTGGCATTGACACGG 59.829 55.000 0.00 0.00 0.00 4.94
1674 9849 0.387565 GGTTGGCATTGACACGGTTT 59.612 50.000 0.00 0.00 0.00 3.27
1675 9850 1.486439 GTTGGCATTGACACGGTTTG 58.514 50.000 0.00 0.00 0.00 2.93
1677 9852 1.372872 GGCATTGACACGGTTTGCC 60.373 57.895 0.00 0.00 45.31 4.52
1679 9854 0.664166 GCATTGACACGGTTTGCCTG 60.664 55.000 0.00 0.00 0.00 4.85
1714 9889 1.082169 GCATGCAAAACAGCGACGA 60.082 52.632 14.21 0.00 37.31 4.20
1733 9908 2.517402 GTGTGGGAACGTTGGGCA 60.517 61.111 5.00 0.00 0.00 5.36
1738 9913 0.322098 TGGGAACGTTGGGCATACTG 60.322 55.000 5.00 0.00 0.00 2.74
1745 9920 0.546598 GTTGGGCATACTGCTACCCT 59.453 55.000 0.00 0.00 44.28 4.34
1774 9949 0.105408 AAGTTTACGGCGTCACCAGT 59.895 50.000 19.21 0.00 39.03 4.00
1797 9972 3.050354 AACCCTGTGTTCCACCGCA 62.050 57.895 0.00 0.00 32.73 5.69
1802 9977 1.845809 CTGTGTTCCACCGCAGCTTC 61.846 60.000 0.00 0.00 36.29 3.86
1817 9992 5.391523 CCGCAGCTTCATCTATCTACTACTC 60.392 48.000 0.00 0.00 0.00 2.59
1880 10055 7.324616 CACGAAGAAGGATTTGAAATTCTTGAC 59.675 37.037 15.80 3.21 40.97 3.18
1886 10061 4.931601 GGATTTGAAATTCTTGACAAGCCC 59.068 41.667 10.50 0.00 0.00 5.19
1889 10064 3.303938 TGAAATTCTTGACAAGCCCCAA 58.696 40.909 10.50 0.00 0.00 4.12
1925 10100 4.803098 ATACGAAGACAGCTACTTGGTT 57.197 40.909 19.32 9.52 37.46 3.67
1939 10114 3.468063 GGTTGAGTCCGACCAGGT 58.532 61.111 0.00 0.00 44.71 4.00
2108 10285 4.223477 ACTGCCATTAAGTCCATGCAAAAT 59.777 37.500 0.00 0.00 0.00 1.82
2216 10396 2.032722 GTCACGGCGTGTTGATAACAAA 60.033 45.455 35.65 12.97 44.16 2.83
2217 10397 2.612672 TCACGGCGTGTTGATAACAAAA 59.387 40.909 35.65 12.44 44.16 2.44
2546 11172 1.326548 GCGTGGAACTAAATAGGCACG 59.673 52.381 0.00 0.00 37.78 5.34
2674 11301 6.432607 ACATGTGAAGACTTGCATCATTAG 57.567 37.500 0.00 0.00 31.78 1.73
2794 11440 8.846943 AGACACCGAAAATCATTGCATATATA 57.153 30.769 0.00 0.00 0.00 0.86
2824 11470 8.647226 CATTTTCTTTTTCAAGAACAAACGACT 58.353 29.630 0.00 0.00 46.71 4.18
2840 11486 6.457676 CAAACGACTGTTGTTTGTCATTTTC 58.542 36.000 31.67 0.00 46.87 2.29
2845 11491 7.431084 ACGACTGTTGTTTGTCATTTTCATTAC 59.569 33.333 0.00 0.00 33.18 1.89
2899 11545 5.831449 GGCCAAGTCTAGATTTGGACCCC 62.831 56.522 37.71 28.21 46.90 4.95
2913 11559 1.710816 GACCCCCAATTTTGACACCA 58.289 50.000 0.00 0.00 0.00 4.17
2923 11569 3.502191 TTTTGACACCAGACAACTTGC 57.498 42.857 0.00 0.00 0.00 4.01
2933 11579 1.000993 ACAACTTGCACCCCCAACA 59.999 52.632 0.00 0.00 0.00 3.33
2949 11595 3.574614 CCAACAATTGAAACCGGACATC 58.425 45.455 13.59 3.39 0.00 3.06
2972 11618 3.396260 TTGTCCCTAGTCTCGGTTTTG 57.604 47.619 0.00 0.00 0.00 2.44
2997 11643 1.650242 TTTTGGTGCTGACTCCCCCA 61.650 55.000 0.00 0.00 0.00 4.96
3018 11664 2.158623 AGTTTTGACCCATGCTGACTCA 60.159 45.455 0.00 0.00 0.00 3.41
3019 11665 2.622942 GTTTTGACCCATGCTGACTCAA 59.377 45.455 0.00 0.00 0.00 3.02
3020 11666 2.189594 TTGACCCATGCTGACTCAAG 57.810 50.000 0.00 0.00 0.00 3.02
3026 11672 1.150827 CATGCTGACTCAAGTTCGCA 58.849 50.000 8.93 8.93 37.69 5.10
3030 11676 3.398406 TGCTGACTCAAGTTCGCATAAA 58.602 40.909 3.99 0.00 31.72 1.40
3043 11689 7.581011 AGTTCGCATAAACAAATTCAAATCC 57.419 32.000 0.00 0.00 0.00 3.01
3044 11690 7.151308 AGTTCGCATAAACAAATTCAAATCCA 58.849 30.769 0.00 0.00 0.00 3.41
3101 11747 5.564048 TCCGTTTATTTTCCCCAAATACG 57.436 39.130 0.00 0.00 37.11 3.06
3105 11751 4.619437 TTATTTTCCCCAAATACGCGTC 57.381 40.909 18.63 0.00 37.11 5.19
3125 11771 5.063817 GCGTCCTTTATTTAGAACCGCTTAA 59.936 40.000 0.00 0.00 36.03 1.85
3199 11845 5.710513 TGTGTAATTGCTTCAAATCTGCT 57.289 34.783 0.00 0.00 0.00 4.24
3226 11872 5.208121 TGTTTCAAATCCCAGAACTCCTTT 58.792 37.500 0.00 0.00 0.00 3.11
3229 11875 7.343316 TGTTTCAAATCCCAGAACTCCTTTAAA 59.657 33.333 0.00 0.00 0.00 1.52
3230 11876 7.906199 TTCAAATCCCAGAACTCCTTTAAAA 57.094 32.000 0.00 0.00 0.00 1.52
3234 11880 8.992073 CAAATCCCAGAACTCCTTTAAAATTTG 58.008 33.333 0.00 0.00 0.00 2.32
3276 11922 5.564063 GCGTACTTTTCCAAGTTTGCCTAAT 60.564 40.000 0.00 0.00 40.66 1.73
3277 11923 6.443792 CGTACTTTTCCAAGTTTGCCTAATT 58.556 36.000 0.00 0.00 40.66 1.40
3308 11954 7.814107 TCAAATTCCTGCAATGTTTGACTAATC 59.186 33.333 10.39 0.00 34.82 1.75
3309 11955 6.839124 ATTCCTGCAATGTTTGACTAATCA 57.161 33.333 0.00 0.00 0.00 2.57
3310 11956 5.627499 TCCTGCAATGTTTGACTAATCAC 57.373 39.130 0.00 0.00 33.38 3.06
3311 11957 4.154015 TCCTGCAATGTTTGACTAATCACG 59.846 41.667 0.00 0.00 33.38 4.35
3312 11958 4.083324 CCTGCAATGTTTGACTAATCACGT 60.083 41.667 0.00 0.00 33.38 4.49
3359 12005 5.543714 TGTATTGTCCACGTTTCATGTACT 58.456 37.500 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 4040 2.003301 GCCAGCTCGGTCTAAGAAAAG 58.997 52.381 4.45 0.00 36.97 2.27
62 4080 1.922189 CGATAGTTGCCGCGGTTAC 59.078 57.895 28.70 23.53 0.00 2.50
298 4316 2.571653 CTGGAGTTCTCACCATACCCAA 59.428 50.000 2.24 0.00 34.11 4.12
317 4335 1.139989 AACGTCAGATTGTCGCACTG 58.860 50.000 0.00 0.00 32.42 3.66
322 4340 3.124636 CCCCTTTAAACGTCAGATTGTCG 59.875 47.826 0.00 0.00 35.19 4.35
339 4357 1.135721 GTTCTACGCATACGACCCCTT 59.864 52.381 0.00 0.00 43.93 3.95
527 4556 2.723746 CAAGCCGCACAAAGCAGT 59.276 55.556 0.00 0.00 46.13 4.40
737 4781 3.173240 GAGGCAAGCGACGACGAC 61.173 66.667 12.29 2.46 42.66 4.34
746 4790 3.869272 CATGACGGCGAGGCAAGC 61.869 66.667 16.62 0.00 44.01 4.01
747 4791 2.034879 AACATGACGGCGAGGCAAG 61.035 57.895 16.62 8.33 44.01 4.01
748 4792 2.031919 AACATGACGGCGAGGCAA 59.968 55.556 16.62 0.00 44.01 4.52
749 4793 2.741985 CAACATGACGGCGAGGCA 60.742 61.111 16.62 9.26 45.56 4.75
750 4794 3.499737 CCAACATGACGGCGAGGC 61.500 66.667 16.62 2.67 0.00 4.70
751 4795 2.047274 ACCAACATGACGGCGAGG 60.047 61.111 16.62 5.92 0.00 4.63
752 4796 2.444624 CGACCAACATGACGGCGAG 61.445 63.158 16.62 2.56 0.00 5.03
753 4797 2.431771 CGACCAACATGACGGCGA 60.432 61.111 16.62 0.00 0.00 5.54
754 4798 2.726691 GACGACCAACATGACGGCG 61.727 63.158 4.80 4.80 0.00 6.46
755 4799 2.726691 CGACGACCAACATGACGGC 61.727 63.158 0.00 0.00 0.00 5.68
877 4921 2.592574 AGGGACACGACGTGACGA 60.593 61.111 33.12 0.00 36.96 4.20
878 4922 2.428569 CAGGGACACGACGTGACG 60.429 66.667 33.12 11.65 36.96 4.35
879 4923 2.733593 GCAGGGACACGACGTGAC 60.734 66.667 33.12 26.22 36.96 3.67
880 4924 2.299503 TTTGCAGGGACACGACGTGA 62.300 55.000 33.12 7.10 36.96 4.35
881 4925 1.831389 CTTTGCAGGGACACGACGTG 61.831 60.000 25.72 25.72 39.75 4.49
882 4926 1.594293 CTTTGCAGGGACACGACGT 60.594 57.895 0.00 0.00 0.00 4.34
883 4927 1.157870 AACTTTGCAGGGACACGACG 61.158 55.000 0.00 0.00 0.00 5.12
884 4928 1.021968 AAACTTTGCAGGGACACGAC 58.978 50.000 0.00 0.00 0.00 4.34
885 4929 1.673920 GAAAACTTTGCAGGGACACGA 59.326 47.619 0.00 0.00 0.00 4.35
889 4933 6.423905 GGAAATTAAGAAAACTTTGCAGGGAC 59.576 38.462 0.00 0.00 0.00 4.46
920 5064 2.732412 ACGGATCTCGCATAGATTGG 57.268 50.000 3.85 0.00 45.35 3.16
921 5065 3.191581 AGGTACGGATCTCGCATAGATTG 59.808 47.826 3.85 0.45 45.35 2.67
924 5068 2.563261 AGGTACGGATCTCGCATAGA 57.437 50.000 3.85 0.00 43.89 1.98
926 5070 2.295349 GGAAAGGTACGGATCTCGCATA 59.705 50.000 3.85 0.00 43.89 3.14
927 5071 1.068741 GGAAAGGTACGGATCTCGCAT 59.931 52.381 3.85 0.00 43.89 4.73
931 5075 3.032459 AGAAGGGAAAGGTACGGATCTC 58.968 50.000 0.00 0.00 0.00 2.75
933 5077 5.548181 AATAGAAGGGAAAGGTACGGATC 57.452 43.478 0.00 0.00 0.00 3.36
934 5078 5.970501 AAATAGAAGGGAAAGGTACGGAT 57.029 39.130 0.00 0.00 0.00 4.18
935 5079 5.767277 AAAATAGAAGGGAAAGGTACGGA 57.233 39.130 0.00 0.00 0.00 4.69
936 5080 7.052248 ACATAAAATAGAAGGGAAAGGTACGG 58.948 38.462 0.00 0.00 0.00 4.02
937 5081 9.774413 ATACATAAAATAGAAGGGAAAGGTACG 57.226 33.333 0.00 0.00 0.00 3.67
970 6810 2.158645 GCAAACGGCAACACAAACTTTT 59.841 40.909 0.00 0.00 43.97 2.27
1011 6858 1.074872 CGGAACCTAAACCTCGCGTC 61.075 60.000 5.77 0.00 0.00 5.19
1013 6860 1.808390 CCGGAACCTAAACCTCGCG 60.808 63.158 0.00 0.00 0.00 5.87
1014 6861 1.449070 CCCGGAACCTAAACCTCGC 60.449 63.158 0.73 0.00 0.00 5.03
1015 6862 0.108472 GACCCGGAACCTAAACCTCG 60.108 60.000 0.73 0.00 0.00 4.63
1016 6863 0.108472 CGACCCGGAACCTAAACCTC 60.108 60.000 0.73 0.00 0.00 3.85
1017 6864 1.977685 CGACCCGGAACCTAAACCT 59.022 57.895 0.73 0.00 0.00 3.50
1018 6865 4.604114 CGACCCGGAACCTAAACC 57.396 61.111 0.73 0.00 0.00 3.27
1056 6908 0.671781 GGAAGCAGCAGATGACACGT 60.672 55.000 0.00 0.00 0.00 4.49
1057 6909 0.390866 AGGAAGCAGCAGATGACACG 60.391 55.000 0.00 0.00 0.00 4.49
1058 6910 2.093764 AGTAGGAAGCAGCAGATGACAC 60.094 50.000 0.00 0.00 0.00 3.67
1059 6911 2.167281 GAGTAGGAAGCAGCAGATGACA 59.833 50.000 0.00 0.00 0.00 3.58
1060 6912 2.797792 CGAGTAGGAAGCAGCAGATGAC 60.798 54.545 0.00 0.00 0.00 3.06
1061 6913 1.406898 CGAGTAGGAAGCAGCAGATGA 59.593 52.381 0.00 0.00 0.00 2.92
1099 6957 9.520515 TTATGCTAAAATTTCTCTCTTGGAGTT 57.479 29.630 0.00 0.00 42.40 3.01
1100 6958 9.520515 TTTATGCTAAAATTTCTCTCTTGGAGT 57.479 29.630 0.00 0.00 42.40 3.85
1122 6980 4.433186 CTGGATCTCGATCGAGCTTTAT 57.567 45.455 34.92 24.62 41.71 1.40
1133 7018 4.193334 CGTGCGGCTGGATCTCGA 62.193 66.667 0.00 0.00 0.00 4.04
1134 7019 3.120979 TACGTGCGGCTGGATCTCG 62.121 63.158 0.00 0.00 0.00 4.04
1137 7022 2.954868 CGTACGTGCGGCTGGATC 60.955 66.667 18.81 0.00 0.00 3.36
1152 7037 9.925865 CGTTTCAAAAATAAATAAATAACGCGT 57.074 25.926 5.58 5.58 0.00 6.01
1218 7133 1.352156 CTCCTCTAACCGCACAACGC 61.352 60.000 0.00 0.00 41.76 4.84
1219 7134 0.242825 TCTCCTCTAACCGCACAACG 59.757 55.000 0.00 0.00 43.15 4.10
1220 7135 1.544691 TCTCTCCTCTAACCGCACAAC 59.455 52.381 0.00 0.00 0.00 3.32
1221 7136 1.544691 GTCTCTCCTCTAACCGCACAA 59.455 52.381 0.00 0.00 0.00 3.33
1222 7137 1.174783 GTCTCTCCTCTAACCGCACA 58.825 55.000 0.00 0.00 0.00 4.57
1223 7138 0.099082 CGTCTCTCCTCTAACCGCAC 59.901 60.000 0.00 0.00 0.00 5.34
1224 7139 0.322277 ACGTCTCTCCTCTAACCGCA 60.322 55.000 0.00 0.00 0.00 5.69
1225 7140 0.377905 GACGTCTCTCCTCTAACCGC 59.622 60.000 8.70 0.00 0.00 5.68
1226 7141 0.651551 CGACGTCTCTCCTCTAACCG 59.348 60.000 14.70 0.00 0.00 4.44
1227 7142 0.377905 GCGACGTCTCTCCTCTAACC 59.622 60.000 14.70 0.00 0.00 2.85
1228 7143 0.026544 CGCGACGTCTCTCCTCTAAC 59.973 60.000 14.70 0.00 0.00 2.34
1229 7144 0.108472 TCGCGACGTCTCTCCTCTAA 60.108 55.000 14.70 0.00 0.00 2.10
1230 7145 0.104487 ATCGCGACGTCTCTCCTCTA 59.896 55.000 12.93 0.00 0.00 2.43
1231 7146 1.153329 ATCGCGACGTCTCTCCTCT 60.153 57.895 12.93 0.00 0.00 3.69
1232 7147 1.010574 CATCGCGACGTCTCTCCTC 60.011 63.158 12.93 0.00 0.00 3.71
1233 7148 1.707239 GACATCGCGACGTCTCTCCT 61.707 60.000 26.48 0.00 0.00 3.69
1234 7149 1.297745 GACATCGCGACGTCTCTCC 60.298 63.158 26.48 1.31 0.00 3.71
1235 7150 1.648756 CGACATCGCGACGTCTCTC 60.649 63.158 29.59 7.67 0.00 3.20
1322 7245 2.668550 GCGAAACTCGGGTGGCTT 60.669 61.111 0.00 0.00 40.84 4.35
1436 9608 1.693627 AGGGACTGTAGTAGCGGATG 58.306 55.000 0.00 0.00 37.18 3.51
1437 9609 2.442502 AGTAGGGACTGTAGTAGCGGAT 59.557 50.000 0.00 0.00 41.52 4.18
1496 9668 3.207669 CAGATCTTGGCGCCAGGC 61.208 66.667 32.14 19.72 44.11 4.85
1522 9694 0.523072 TAGTGTCACGTACCTTCCGC 59.477 55.000 0.00 0.00 0.00 5.54
1533 9705 2.733227 GCTTTGGCATGCATAGTGTCAC 60.733 50.000 21.36 0.00 38.54 3.67
1535 9707 1.473677 TGCTTTGGCATGCATAGTGTC 59.526 47.619 21.36 0.00 44.28 3.67
1548 9720 5.392380 GGTCAACATTGAGTATCTGCTTTGG 60.392 44.000 0.00 0.00 37.98 3.28
1556 9728 6.150140 AGCTCAAAAGGTCAACATTGAGTATC 59.850 38.462 13.87 0.98 46.56 2.24
1559 9731 4.210331 AGCTCAAAAGGTCAACATTGAGT 58.790 39.130 13.87 1.60 46.56 3.41
1575 9747 3.688185 AGATAGTCGTTGTCGTAGCTCAA 59.312 43.478 0.00 0.00 38.33 3.02
1579 9751 2.110226 GCAGATAGTCGTTGTCGTAGC 58.890 52.381 0.00 0.00 38.33 3.58
1581 9753 2.086094 TGGCAGATAGTCGTTGTCGTA 58.914 47.619 0.00 0.00 38.33 3.43
1587 9759 4.830046 AGATATCAGTGGCAGATAGTCGTT 59.170 41.667 5.32 0.00 32.00 3.85
1588 9760 4.402829 AGATATCAGTGGCAGATAGTCGT 58.597 43.478 5.32 0.00 32.00 4.34
1590 9762 5.953183 CTGAGATATCAGTGGCAGATAGTC 58.047 45.833 9.26 0.00 32.00 2.59
1603 9775 4.680708 GCTCAAACCGGAACTGAGATATCA 60.681 45.833 25.89 0.00 39.15 2.15
1607 9779 1.347707 TGCTCAAACCGGAACTGAGAT 59.652 47.619 25.89 0.00 39.15 2.75
1616 9788 2.225068 AGACGATATGCTCAAACCGG 57.775 50.000 0.00 0.00 0.00 5.28
1617 9789 2.719556 CGTAGACGATATGCTCAAACCG 59.280 50.000 0.00 0.00 43.02 4.44
1640 9815 0.027979 CAACCATCTTGCGCATACCG 59.972 55.000 12.75 0.00 40.75 4.02
1647 9822 0.527113 TCAATGCCAACCATCTTGCG 59.473 50.000 0.00 0.00 31.43 4.85
1656 9831 1.486439 CAAACCGTGTCAATGCCAAC 58.514 50.000 0.00 0.00 0.00 3.77
1658 9833 1.361993 GCAAACCGTGTCAATGCCA 59.638 52.632 0.00 0.00 0.00 4.92
1671 9846 1.615392 ACCAATCTCTTGCAGGCAAAC 59.385 47.619 8.20 0.00 35.33 2.93
1674 9849 1.250328 CAACCAATCTCTTGCAGGCA 58.750 50.000 0.00 0.00 0.00 4.75
1675 9850 1.251251 ACAACCAATCTCTTGCAGGC 58.749 50.000 0.00 0.00 0.00 4.85
1677 9852 2.034939 TGCAACAACCAATCTCTTGCAG 59.965 45.455 0.00 0.00 41.67 4.41
1679 9854 2.798976 TGCAACAACCAATCTCTTGC 57.201 45.000 0.00 0.00 38.16 4.01
1714 9889 2.513895 CCCAACGTTCCCACACCT 59.486 61.111 0.00 0.00 0.00 4.00
1733 9908 2.292257 TGTCCTGTCAGGGTAGCAGTAT 60.292 50.000 19.11 0.00 35.59 2.12
1738 9913 1.348036 ACTTTGTCCTGTCAGGGTAGC 59.652 52.381 19.11 7.70 35.59 3.58
1745 9920 2.215196 GCCGTAAACTTTGTCCTGTCA 58.785 47.619 0.00 0.00 0.00 3.58
1774 9949 2.312323 TGGAACACAGGGTTGGACA 58.688 52.632 0.00 0.00 40.63 4.02
1797 9972 7.386848 GTCTTCGAGTAGTAGATAGATGAAGCT 59.613 40.741 0.00 0.00 32.47 3.74
1802 9977 6.157904 TCCGTCTTCGAGTAGTAGATAGATG 58.842 44.000 0.00 0.00 39.71 2.90
1817 9992 1.478137 CGGCTAATCTTCCGTCTTCG 58.522 55.000 0.00 0.00 40.72 3.79
1880 10055 1.665442 CCCGAAACTTTGGGGCTTG 59.335 57.895 8.55 0.00 46.55 4.01
1886 10061 4.451774 TCGTATACAAACCCGAAACTTTGG 59.548 41.667 3.32 0.00 32.57 3.28
1889 10064 5.406477 GTCTTCGTATACAAACCCGAAACTT 59.594 40.000 3.32 0.00 38.66 2.66
1925 10100 1.816863 GCTCAACCTGGTCGGACTCA 61.817 60.000 8.23 3.83 36.31 3.41
1939 10114 0.532573 GAGGACGACCATCAGCTCAA 59.467 55.000 6.71 0.00 38.94 3.02
2216 10396 0.247185 CGCCATTGCCAACCTTCATT 59.753 50.000 0.00 0.00 0.00 2.57
2217 10397 1.892338 CGCCATTGCCAACCTTCAT 59.108 52.632 0.00 0.00 0.00 2.57
2554 11180 2.281070 GCATGATGATCGGGCGGT 60.281 61.111 0.00 0.00 0.00 5.68
2804 11450 6.362283 ACAACAGTCGTTTGTTCTTGAAAAAG 59.638 34.615 4.69 0.00 39.17 2.27
2819 11465 5.303747 TGAAAATGACAAACAACAGTCGT 57.696 34.783 0.00 0.00 37.58 4.34
2824 11470 9.645059 TTTCTGTAATGAAAATGACAAACAACA 57.355 25.926 0.00 0.00 33.59 3.33
2852 11498 8.669243 CCAAGAGTTGAAGGATGAAAAGTATAC 58.331 37.037 0.00 0.00 0.00 1.47
2867 11513 3.646162 TCTAGACTTGGCCAAGAGTTGAA 59.354 43.478 44.50 24.55 40.79 2.69
2899 11545 4.654091 AGTTGTCTGGTGTCAAAATTGG 57.346 40.909 0.00 0.00 0.00 3.16
2909 11555 1.455383 GGGGTGCAAGTTGTCTGGTG 61.455 60.000 4.48 0.00 0.00 4.17
2913 11559 0.755327 GTTGGGGGTGCAAGTTGTCT 60.755 55.000 4.48 0.00 0.00 3.41
2923 11569 1.270041 CGGTTTCAATTGTTGGGGGTG 60.270 52.381 5.13 0.00 0.00 4.61
2949 11595 0.886563 ACCGAGACTAGGGACAAACG 59.113 55.000 6.56 0.00 0.00 3.60
2972 11618 0.818040 AGTCAGCACCAAAACCGGTC 60.818 55.000 8.04 0.00 37.07 4.79
2997 11643 2.158623 TGAGTCAGCATGGGTCAAAACT 60.159 45.455 0.00 0.00 36.16 2.66
3018 11664 7.655328 TGGATTTGAATTTGTTTATGCGAACTT 59.345 29.630 0.00 0.00 0.00 2.66
3019 11665 7.151308 TGGATTTGAATTTGTTTATGCGAACT 58.849 30.769 0.00 0.00 0.00 3.01
3020 11666 7.344910 TGGATTTGAATTTGTTTATGCGAAC 57.655 32.000 0.00 0.00 0.00 3.95
3026 11672 9.729281 AAAGCTCATGGATTTGAATTTGTTTAT 57.271 25.926 0.00 0.00 31.85 1.40
3091 11737 2.027003 TAAAGGACGCGTATTTGGGG 57.973 50.000 24.42 0.00 0.00 4.96
3101 11747 2.934553 AGCGGTTCTAAATAAAGGACGC 59.065 45.455 0.00 0.00 0.00 5.19
3177 11823 5.710513 AGCAGATTTGAAGCAATTACACA 57.289 34.783 0.00 0.00 0.00 3.72
3187 11833 8.807667 ATTTGAAACAGTAAGCAGATTTGAAG 57.192 30.769 0.00 0.00 0.00 3.02
3199 11845 5.768164 GGAGTTCTGGGATTTGAAACAGTAA 59.232 40.000 0.00 0.00 32.92 2.24
3229 11875 9.959749 ACGCGGATTATAAATAATTCACAAATT 57.040 25.926 12.47 0.00 38.61 1.82
3282 11928 5.534207 AGTCAAACATTGCAGGAATTTGA 57.466 34.783 11.30 11.30 37.03 2.69
3336 11982 5.407084 CAGTACATGAAACGTGGACAATACA 59.593 40.000 0.00 0.00 32.69 2.29
3344 11990 3.362596 CGTGAACAGTACATGAAACGTGG 60.363 47.826 0.00 0.00 32.11 4.94
3346 11992 3.450578 ACGTGAACAGTACATGAAACGT 58.549 40.909 0.00 9.37 39.27 3.99


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

AutoCloner maintained by Alex Coulton.