Multiple sequence alignment - TraesCS3B01G525000

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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 TraesCS3B01G525000 chr3B 100.000 3131 0 0 1 3131 766786400 766783270 0.000000e+00 5782.0
1 TraesCS3B01G525000 chr3B 94.746 1161 54 5 1140 2296 768341461 768342618 0.000000e+00 1799.0
2 TraesCS3B01G525000 chr3B 89.200 1000 60 9 1 970 768340380 768341361 0.000000e+00 1205.0
3 TraesCS3B01G525000 chr3B 74.464 932 198 30 1214 2122 773843722 773844636 1.770000e-97 366.0
4 TraesCS3B01G525000 chr3B 73.489 943 212 28 1205 2126 771171544 771172469 3.900000e-84 322.0
5 TraesCS3B01G525000 chr3B 73.326 941 217 23 1205 2126 770969763 770968838 1.810000e-82 316.0
6 TraesCS3B01G525000 chr3B 73.431 956 202 41 1205 2128 771533475 771532540 8.430000e-81 311.0
7 TraesCS3B01G525000 chr3B 72.389 967 199 53 1200 2127 770653294 770652357 8.670000e-61 244.0
8 TraesCS3B01G525000 chr3B 91.608 143 12 0 1961 2103 766659767 766659625 6.850000e-47 198.0
9 TraesCS3B01G525000 chr3B 84.153 183 26 3 2320 2501 766654453 766654273 1.150000e-39 174.0
10 TraesCS3B01G525000 chr3B 73.258 445 103 12 1659 2092 802999223 802999662 7.000000e-32 148.0
11 TraesCS3B01G525000 chr3D 92.212 1361 60 21 958 2307 575759989 575758664 0.000000e+00 1884.0
12 TraesCS3B01G525000 chr3D 89.755 449 19 8 475 905 575760455 575760016 1.640000e-152 549.0
13 TraesCS3B01G525000 chr3D 87.660 470 39 5 2311 2775 575758694 575758239 2.140000e-146 529.0
14 TraesCS3B01G525000 chr3D 74.681 940 191 35 1214 2126 579429346 579430265 1.060000e-99 374.0
15 TraesCS3B01G525000 chr3D 73.545 945 215 25 1205 2130 577790170 577789242 8.370000e-86 327.0
16 TraesCS3B01G525000 chr3D 73.153 961 209 33 1205 2134 578243572 578242630 1.830000e-77 300.0
17 TraesCS3B01G525000 chr3D 72.737 950 197 38 1205 2130 577969147 577970058 2.390000e-66 263.0
18 TraesCS3B01G525000 chr3D 72.565 955 199 50 1200 2121 577414676 577413752 1.440000e-63 254.0
19 TraesCS3B01G525000 chr3A 95.435 1161 45 4 1140 2296 711297428 711296272 0.000000e+00 1844.0
20 TraesCS3B01G525000 chr3A 90.534 824 70 6 2311 3130 711296289 711295470 0.000000e+00 1083.0
21 TraesCS3B01G525000 chr3A 87.711 651 51 22 475 1104 711298064 711297422 0.000000e+00 732.0
22 TraesCS3B01G525000 chr3A 74.947 938 192 32 1214 2126 714614906 714615825 1.050000e-104 390.0
23 TraesCS3B01G525000 chr3A 73.817 951 202 32 1205 2130 713535477 713534549 1.800000e-87 333.0
24 TraesCS3B01G525000 chr3A 72.321 896 181 51 1268 2128 712729265 712728402 5.260000e-53 219.0
25 TraesCS3B01G525000 chrUn 74.464 932 198 30 1214 2122 41302670 41303584 1.770000e-97 366.0
26 TraesCS3B01G525000 chrUn 82.195 410 53 17 2672 3075 7636576 7636971 5.000000e-88 335.0
27 TraesCS3B01G525000 chr7D 83.668 398 55 8 2667 3060 599869799 599870190 1.770000e-97 366.0
28 TraesCS3B01G525000 chr1D 83.459 399 52 10 2675 3068 436861036 436860647 2.970000e-95 359.0
29 TraesCS3B01G525000 chr6D 83.250 400 55 9 2672 3068 364497761 364498151 1.070000e-94 357.0
30 TraesCS3B01G525000 chr2A 83.503 394 54 9 2675 3062 28210811 28210423 1.070000e-94 357.0
31 TraesCS3B01G525000 chr7A 81.863 408 59 10 2661 3063 681581366 681581763 2.330000e-86 329.0
32 TraesCS3B01G525000 chr2D 81.401 414 64 10 2667 3075 446896281 446895876 3.010000e-85 326.0
33 TraesCS3B01G525000 chr2D 86.364 66 7 2 305 369 355631242 355631178 1.560000e-08 71.3
34 TraesCS3B01G525000 chr1A 84.478 335 46 6 2739 3071 329583252 329582922 3.010000e-85 326.0
35 TraesCS3B01G525000 chr5B 87.931 58 4 3 297 351 629950224 629950281 7.250000e-07 65.8
36 TraesCS3B01G525000 chr1B 91.304 46 2 2 318 361 24262712 24262757 9.380000e-06 62.1
37 TraesCS3B01G525000 chr6A 90.909 44 2 2 309 350 107687884 107687841 1.210000e-04 58.4
38 TraesCS3B01G525000 chr2B 88.889 45 2 2 309 350 725663747 725663791 6.000000e-03 52.8


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 TraesCS3B01G525000 chr3B 766783270 766786400 3130 True 5782.000000 5782 100.000000 1 3131 1 chr3B.!!$R3 3130
1 TraesCS3B01G525000 chr3B 768340380 768342618 2238 False 1502.000000 1799 91.973000 1 2296 2 chr3B.!!$F4 2295
2 TraesCS3B01G525000 chr3B 773843722 773844636 914 False 366.000000 366 74.464000 1214 2122 1 chr3B.!!$F2 908
3 TraesCS3B01G525000 chr3B 771171544 771172469 925 False 322.000000 322 73.489000 1205 2126 1 chr3B.!!$F1 921
4 TraesCS3B01G525000 chr3B 770968838 770969763 925 True 316.000000 316 73.326000 1205 2126 1 chr3B.!!$R5 921
5 TraesCS3B01G525000 chr3B 771532540 771533475 935 True 311.000000 311 73.431000 1205 2128 1 chr3B.!!$R6 923
6 TraesCS3B01G525000 chr3B 770652357 770653294 937 True 244.000000 244 72.389000 1200 2127 1 chr3B.!!$R4 927
7 TraesCS3B01G525000 chr3D 575758239 575760455 2216 True 987.333333 1884 89.875667 475 2775 3 chr3D.!!$R4 2300
8 TraesCS3B01G525000 chr3D 579429346 579430265 919 False 374.000000 374 74.681000 1214 2126 1 chr3D.!!$F2 912
9 TraesCS3B01G525000 chr3D 577789242 577790170 928 True 327.000000 327 73.545000 1205 2130 1 chr3D.!!$R2 925
10 TraesCS3B01G525000 chr3D 578242630 578243572 942 True 300.000000 300 73.153000 1205 2134 1 chr3D.!!$R3 929
11 TraesCS3B01G525000 chr3D 577969147 577970058 911 False 263.000000 263 72.737000 1205 2130 1 chr3D.!!$F1 925
12 TraesCS3B01G525000 chr3D 577413752 577414676 924 True 254.000000 254 72.565000 1200 2121 1 chr3D.!!$R1 921
13 TraesCS3B01G525000 chr3A 711295470 711298064 2594 True 1219.666667 1844 91.226667 475 3130 3 chr3A.!!$R3 2655
14 TraesCS3B01G525000 chr3A 714614906 714615825 919 False 390.000000 390 74.947000 1214 2126 1 chr3A.!!$F1 912
15 TraesCS3B01G525000 chr3A 713534549 713535477 928 True 333.000000 333 73.817000 1205 2130 1 chr3A.!!$R2 925
16 TraesCS3B01G525000 chr3A 712728402 712729265 863 True 219.000000 219 72.321000 1268 2128 1 chr3A.!!$R1 860
17 TraesCS3B01G525000 chrUn 41302670 41303584 914 False 366.000000 366 74.464000 1214 2122 1 chrUn.!!$F2 908

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
226 227 1.403972 GCGGAGTAACGAGCGAACAG 61.404 60.0 0.00 0.00 35.47 3.16 F
1124 1231 0.094730 CGCAGTTAGGTAACGCAAGC 59.905 55.0 13.34 7.85 46.39 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1260 1373 0.243907 GGTAGAGCTGCACGACTTCA 59.756 55.0 9.73 0.0 0.0 3.02 R
3034 3191 0.676184 AGAAGTGTGCAAGCTCGAGA 59.324 50.0 18.75 0.0 0.0 4.04 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
56 57 9.716507 ATAAATATTCTTTCAAATTCGTGGACG 57.283 29.630 0.00 0.00 41.45 4.79
60 61 5.238006 TCTTTCAAATTCGTGGACGTTTT 57.762 34.783 0.00 0.00 40.80 2.43
95 96 7.167968 CACCGATTATTTAAAGCCATGAACATG 59.832 37.037 7.70 7.70 38.51 3.21
96 97 7.147915 ACCGATTATTTAAAGCCATGAACATGT 60.148 33.333 12.74 0.00 37.11 3.21
135 136 9.927668 ACCATTTCAAAATTAGTAACAGATTGG 57.072 29.630 0.00 0.00 0.00 3.16
161 162 3.181510 CCATAAAACAGCGAACCAGTAGC 60.182 47.826 0.00 0.00 0.00 3.58
175 176 6.183360 CGAACCAGTAGCAACAGAGAAATAAG 60.183 42.308 0.00 0.00 0.00 1.73
178 179 6.876257 ACCAGTAGCAACAGAGAAATAAGAAG 59.124 38.462 0.00 0.00 0.00 2.85
181 182 8.655092 CAGTAGCAACAGAGAAATAAGAAGAAG 58.345 37.037 0.00 0.00 0.00 2.85
183 184 9.209175 GTAGCAACAGAGAAATAAGAAGAAGAA 57.791 33.333 0.00 0.00 0.00 2.52
195 196 2.289002 AGAAGAAGAAAACAGCGTGCAG 59.711 45.455 0.00 0.00 0.00 4.41
226 227 1.403972 GCGGAGTAACGAGCGAACAG 61.404 60.000 0.00 0.00 35.47 3.16
245 246 2.412089 CAGCGCAAAGTAGTGACCTTAC 59.588 50.000 11.47 0.00 0.00 2.34
249 250 2.412089 GCAAAGTAGTGACCTTACTGCG 59.588 50.000 0.00 0.00 38.18 5.18
255 256 4.789075 GACCTTACTGCGCCGCGA 62.789 66.667 18.91 0.50 0.00 5.87
325 326 2.383855 AGATGTGGCTAGGTCTCAGTC 58.616 52.381 0.00 0.00 0.00 3.51
517 548 4.483950 TCCAAAACCATTACCATCAACCA 58.516 39.130 0.00 0.00 0.00 3.67
519 550 6.256819 TCCAAAACCATTACCATCAACCATA 58.743 36.000 0.00 0.00 0.00 2.74
520 551 6.379703 TCCAAAACCATTACCATCAACCATAG 59.620 38.462 0.00 0.00 0.00 2.23
522 553 7.093552 CCAAAACCATTACCATCAACCATAGAA 60.094 37.037 0.00 0.00 0.00 2.10
523 554 7.645058 AAACCATTACCATCAACCATAGAAG 57.355 36.000 0.00 0.00 0.00 2.85
533 564 8.497745 ACCATCAACCATAGAAGATAGAACATT 58.502 33.333 0.00 0.00 0.00 2.71
597 628 2.355115 GGAATTCCACGCCCCAGT 59.645 61.111 20.04 0.00 35.64 4.00
700 732 2.882793 GTAGCTTACGGGCGATGTC 58.117 57.895 0.00 0.00 37.29 3.06
717 749 1.741401 TCTTGCGCCGAACCAGATG 60.741 57.895 4.18 0.00 0.00 2.90
849 900 4.104776 CCAAACTGCCTAATTGCATTACG 58.895 43.478 0.00 0.00 41.16 3.18
917 1018 1.874915 CATGCACGTACGTACCCCG 60.875 63.158 22.34 9.54 44.03 5.73
918 1019 3.067480 ATGCACGTACGTACCCCGG 62.067 63.158 22.34 8.75 42.24 5.73
920 1021 4.496927 CACGTACGTACCCCGGCC 62.497 72.222 22.34 0.00 42.24 6.13
959 1060 6.381420 AGTTTAGGAAGATCTTAGCTGCACTA 59.619 38.462 8.25 0.63 0.00 2.74
963 1064 4.367450 GAAGATCTTAGCTGCACTACTGG 58.633 47.826 8.25 0.00 0.00 4.00
964 1065 3.370104 AGATCTTAGCTGCACTACTGGT 58.630 45.455 1.02 0.00 0.00 4.00
975 1076 3.111853 CACTACTGGTGCAGAGTTTGA 57.888 47.619 3.70 0.00 39.22 2.69
976 1077 3.062763 CACTACTGGTGCAGAGTTTGAG 58.937 50.000 3.70 0.00 39.22 3.02
978 1079 3.895656 ACTACTGGTGCAGAGTTTGAGTA 59.104 43.478 3.70 0.00 35.18 2.59
987 1088 4.238514 GCAGAGTTTGAGTACACGAAGAT 58.761 43.478 0.00 0.00 0.00 2.40
988 1089 4.324936 GCAGAGTTTGAGTACACGAAGATC 59.675 45.833 0.00 0.00 0.00 2.75
989 1090 4.555360 CAGAGTTTGAGTACACGAAGATCG 59.445 45.833 0.00 0.00 46.93 3.69
992 1093 3.482722 TTGAGTACACGAAGATCGACC 57.517 47.619 6.78 0.00 43.74 4.79
999 1100 0.811915 ACGAAGATCGACCAGTGGAG 59.188 55.000 18.40 9.68 43.74 3.86
1000 1101 1.095600 CGAAGATCGACCAGTGGAGA 58.904 55.000 18.40 15.08 43.74 3.71
1001 1102 1.678627 CGAAGATCGACCAGTGGAGAT 59.321 52.381 18.40 19.17 43.74 2.75
1030 1131 1.074319 GCATCGTGCCTGCATGTTTG 61.074 55.000 10.87 10.69 37.42 2.93
1056 1160 1.378762 GTTGGCCCTTGGAGTGCTA 59.621 57.895 0.00 0.00 0.00 3.49
1057 1161 0.678048 GTTGGCCCTTGGAGTGCTAG 60.678 60.000 0.00 0.00 0.00 3.42
1058 1162 2.124529 GGCCCTTGGAGTGCTAGC 60.125 66.667 8.10 8.10 0.00 3.42
1059 1163 2.671070 GCCCTTGGAGTGCTAGCA 59.329 61.111 14.93 14.93 0.00 3.49
1060 1164 1.002134 GCCCTTGGAGTGCTAGCAA 60.002 57.895 21.29 0.00 0.00 3.91
1081 1188 4.046286 ACAATTCCTGCAGGTAATTCCA 57.954 40.909 31.58 8.42 39.02 3.53
1083 1190 4.646492 ACAATTCCTGCAGGTAATTCCATC 59.354 41.667 31.58 0.00 39.02 3.51
1085 1192 2.204463 TCCTGCAGGTAATTCCATCCA 58.796 47.619 31.58 5.39 39.02 3.41
1097 1204 8.506083 AGGTAATTCCATCCACTTCAGATTATT 58.494 33.333 0.00 0.00 39.02 1.40
1106 1213 4.152402 CCACTTCAGATTATTTATCGGGCG 59.848 45.833 0.00 0.00 38.36 6.13
1107 1214 3.746492 ACTTCAGATTATTTATCGGGCGC 59.254 43.478 0.00 0.00 38.36 6.53
1108 1215 3.394674 TCAGATTATTTATCGGGCGCA 57.605 42.857 10.83 0.00 38.36 6.09
1109 1216 3.325870 TCAGATTATTTATCGGGCGCAG 58.674 45.455 10.83 1.95 38.36 5.18
1110 1217 3.067106 CAGATTATTTATCGGGCGCAGT 58.933 45.455 10.83 0.00 38.36 4.40
1111 1218 3.498397 CAGATTATTTATCGGGCGCAGTT 59.502 43.478 10.83 0.00 38.36 3.16
1112 1219 4.688879 CAGATTATTTATCGGGCGCAGTTA 59.311 41.667 10.83 0.00 38.36 2.24
1113 1220 4.929808 AGATTATTTATCGGGCGCAGTTAG 59.070 41.667 10.83 0.00 38.36 2.34
1114 1221 1.878953 ATTTATCGGGCGCAGTTAGG 58.121 50.000 10.83 0.00 0.00 2.69
1115 1222 0.538118 TTTATCGGGCGCAGTTAGGT 59.462 50.000 10.83 0.00 0.00 3.08
1116 1223 1.401761 TTATCGGGCGCAGTTAGGTA 58.598 50.000 10.83 0.00 0.00 3.08
1117 1224 1.401761 TATCGGGCGCAGTTAGGTAA 58.598 50.000 10.83 0.00 0.00 2.85
1118 1225 0.179092 ATCGGGCGCAGTTAGGTAAC 60.179 55.000 10.83 0.00 36.46 2.50
1119 1226 2.162754 CGGGCGCAGTTAGGTAACG 61.163 63.158 10.83 0.00 46.39 3.18
1124 1231 0.094730 CGCAGTTAGGTAACGCAAGC 59.905 55.000 13.34 7.85 46.39 4.01
1125 1232 1.153353 GCAGTTAGGTAACGCAAGCA 58.847 50.000 10.04 0.00 46.39 3.91
1126 1233 1.128692 GCAGTTAGGTAACGCAAGCAG 59.871 52.381 10.04 0.00 46.39 4.24
1127 1234 1.128692 CAGTTAGGTAACGCAAGCAGC 59.871 52.381 0.00 0.00 46.39 5.25
1128 1235 1.002087 AGTTAGGTAACGCAAGCAGCT 59.998 47.619 0.00 0.00 46.39 4.24
1129 1236 2.232941 AGTTAGGTAACGCAAGCAGCTA 59.767 45.455 0.00 0.00 46.39 3.32
1144 1251 1.002792 CAGCTAGTACGTGCGCTATCA 60.003 52.381 9.73 0.00 0.00 2.15
1146 1253 1.002684 GCTAGTACGTGCGCTATCAGT 60.003 52.381 9.73 3.99 0.00 3.41
1147 1254 2.541178 GCTAGTACGTGCGCTATCAGTT 60.541 50.000 9.73 0.00 0.00 3.16
1148 1255 3.303593 GCTAGTACGTGCGCTATCAGTTA 60.304 47.826 9.73 0.00 0.00 2.24
1155 1262 2.930040 GTGCGCTATCAGTTAAGCAAGA 59.070 45.455 9.73 0.00 38.70 3.02
1159 1266 4.387256 GCGCTATCAGTTAAGCAAGATAGG 59.613 45.833 0.00 0.00 40.01 2.57
1168 1275 6.985059 CAGTTAAGCAAGATAGGGTACTAACC 59.015 42.308 0.00 0.00 45.97 2.85
1182 1289 1.908066 CTAACCCCAGTTGCGCGTTC 61.908 60.000 8.43 0.00 36.68 3.95
1550 1672 1.811266 CCATGCAGAACCTCGACGG 60.811 63.158 0.00 0.03 39.35 4.79
1983 2123 5.241403 ACCAGAACCTGATCAAACATGTA 57.759 39.130 0.00 0.00 32.44 2.29
2240 2388 5.907207 TGTACTTGAATAAGCTGCCTCTAG 58.093 41.667 0.00 0.00 37.43 2.43
2296 2448 4.180817 GCGGAAAAGGTCCCAAATTATTG 58.819 43.478 0.00 0.00 44.60 1.90
2297 2449 4.081917 GCGGAAAAGGTCCCAAATTATTGA 60.082 41.667 0.00 0.00 44.60 2.57
2298 2450 5.567823 GCGGAAAAGGTCCCAAATTATTGAA 60.568 40.000 0.00 0.00 44.60 2.69
2299 2451 5.867174 CGGAAAAGGTCCCAAATTATTGAAC 59.133 40.000 0.00 0.00 44.60 3.18
2300 2452 5.867174 GGAAAAGGTCCCAAATTATTGAACG 59.133 40.000 0.00 0.00 41.10 3.95
2301 2453 4.450082 AAGGTCCCAAATTATTGAACGC 57.550 40.909 0.00 0.00 38.94 4.84
2302 2454 3.426615 AGGTCCCAAATTATTGAACGCA 58.573 40.909 0.00 0.00 38.94 5.24
2303 2455 3.829601 AGGTCCCAAATTATTGAACGCAA 59.170 39.130 0.00 0.00 38.94 4.85
2304 2456 4.282195 AGGTCCCAAATTATTGAACGCAAA 59.718 37.500 0.00 0.00 38.94 3.68
2305 2457 4.991687 GGTCCCAAATTATTGAACGCAAAA 59.008 37.500 0.00 0.00 38.94 2.44
2306 2458 5.467063 GGTCCCAAATTATTGAACGCAAAAA 59.533 36.000 0.00 0.00 38.94 1.94
2365 2520 8.416329 AGCGCTCAAATTATTTAATGGAGAAAT 58.584 29.630 2.64 0.00 33.35 2.17
2395 2550 3.270027 GCACACTGGCAATACTGTGATA 58.730 45.455 10.37 0.00 41.20 2.15
2425 2580 0.667993 CACTTCTTTTTGGCGAGCCA 59.332 50.000 13.49 13.49 45.63 4.75
2434 2589 4.937431 GGCGAGCCATAGGTGCCC 62.937 72.222 9.58 0.00 39.83 5.36
2443 2598 0.179056 CATAGGTGCCCGTTGGGTAG 60.179 60.000 3.40 0.00 46.51 3.18
2463 2618 5.589050 GGTAGTAATTTCACTGGATCAACCC 59.411 44.000 0.00 0.00 38.00 4.11
2472 2627 0.477597 TGGATCAACCCCTCCCTTGT 60.478 55.000 0.00 0.00 38.00 3.16
2536 2692 5.538053 TCAATAGAAAACTCCCACATGCAAA 59.462 36.000 0.00 0.00 0.00 3.68
2605 2762 5.366829 TCGAGGTATATCGTTATGTGTGG 57.633 43.478 0.00 0.00 43.20 4.17
2607 2764 5.708697 TCGAGGTATATCGTTATGTGTGGAT 59.291 40.000 0.00 0.00 43.20 3.41
2652 2809 4.612264 AAGCATCTTTCACCAGCAAAAT 57.388 36.364 0.00 0.00 0.00 1.82
2724 2881 4.836736 AGTATCCGGCCAAATAAGCTAGTA 59.163 41.667 2.24 0.00 0.00 1.82
2777 2934 4.112331 GACCTAGCCCATCCCCTAAATAT 58.888 47.826 0.00 0.00 0.00 1.28
2782 2939 5.941146 AGCCCATCCCCTAAATATAACAA 57.059 39.130 0.00 0.00 0.00 2.83
2823 2980 2.091852 TTGCATTTCATTTTCGGCCC 57.908 45.000 0.00 0.00 0.00 5.80
2832 2989 1.342819 CATTTTCGGCCCCTGAAACAA 59.657 47.619 0.00 0.00 35.22 2.83
2837 2994 1.616374 TCGGCCCCTGAAACAAATTTC 59.384 47.619 0.00 0.00 43.96 2.17
2861 3018 8.451687 TCATTGCTTCTTTATTTCATTGAACG 57.548 30.769 0.00 0.00 0.00 3.95
2922 3079 3.185594 TCGCAACGAGAACGAAATCAAAT 59.814 39.130 0.00 0.00 42.66 2.32
2977 3134 5.068987 ACATATCCAATTTGCATAACCGCTT 59.931 36.000 0.00 0.00 0.00 4.68
3000 3157 9.952188 GCTTCACTAGTTGGATTAATATTTTCC 57.048 33.333 0.00 9.23 0.00 3.13
3031 3188 7.761249 GTCTTCATTGTTAATTCCCTCAATTGG 59.239 37.037 5.42 0.00 35.34 3.16
3033 3190 5.721000 TCATTGTTAATTCCCTCAATTGGCT 59.279 36.000 5.42 0.00 35.34 4.75
3034 3191 6.213195 TCATTGTTAATTCCCTCAATTGGCTT 59.787 34.615 5.42 0.00 35.34 4.35
3052 3209 1.458827 CTTCTCGAGCTTGCACACTTC 59.541 52.381 7.81 0.00 0.00 3.01
3060 3217 3.549794 AGCTTGCACACTTCTTTCTTCT 58.450 40.909 0.00 0.00 0.00 2.85
3071 3228 5.698545 CACTTCTTTCTTCTTCAGTTCCGAT 59.301 40.000 0.00 0.00 0.00 4.18
3085 3242 2.489938 TCCGATGAACAAAAGGAGGG 57.510 50.000 0.00 0.00 0.00 4.30
3101 3258 2.713708 GGAGGGGCTCAAGAATAAGGAT 59.286 50.000 0.00 0.00 31.08 3.24
3102 3259 3.497584 GGAGGGGCTCAAGAATAAGGATG 60.498 52.174 0.00 0.00 31.08 3.51
3105 3262 3.290710 GGGCTCAAGAATAAGGATGCAA 58.709 45.455 0.00 0.00 0.00 4.08
3117 3274 9.370930 AGAATAAGGATGCAATGATAAAATGGA 57.629 29.630 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 5.505446 CGGTGAATTTATAAAAACGTCCACG 59.495 40.000 1.21 0.00 46.33 4.94
95 96 5.427036 TGAAATGGTCCGTGAACTAAAAC 57.573 39.130 0.00 0.00 0.00 2.43
96 97 6.452494 TTTGAAATGGTCCGTGAACTAAAA 57.548 33.333 0.00 0.00 0.00 1.52
134 135 3.004944 TGGTTCGCTGTTTTATGGAAACC 59.995 43.478 0.00 0.00 45.66 3.27
135 136 4.226761 CTGGTTCGCTGTTTTATGGAAAC 58.773 43.478 0.00 0.00 46.28 2.78
139 140 3.181510 GCTACTGGTTCGCTGTTTTATGG 60.182 47.826 0.00 0.00 0.00 2.74
150 151 2.724977 TCTCTGTTGCTACTGGTTCG 57.275 50.000 5.45 0.00 0.00 3.95
175 176 2.644078 CTGCACGCTGTTTTCTTCTTC 58.356 47.619 0.00 0.00 0.00 2.87
178 179 0.993746 CGCTGCACGCTGTTTTCTTC 60.994 55.000 0.00 0.00 36.13 2.87
181 182 1.010125 TTCGCTGCACGCTGTTTTC 60.010 52.632 0.00 0.00 43.23 2.29
183 184 2.327940 GTTCGCTGCACGCTGTTT 59.672 55.556 0.00 0.00 43.23 2.83
202 203 3.823330 CTCGTTACTCCGCCCGCT 61.823 66.667 0.00 0.00 0.00 5.52
206 207 2.157073 GTTCGCTCGTTACTCCGCC 61.157 63.158 0.00 0.00 0.00 6.13
208 209 1.403972 GCTGTTCGCTCGTTACTCCG 61.404 60.000 0.00 0.00 35.14 4.63
226 227 2.412089 CAGTAAGGTCACTACTTTGCGC 59.588 50.000 0.00 0.00 33.43 6.09
233 234 0.801067 CGGCGCAGTAAGGTCACTAC 60.801 60.000 10.83 0.00 0.00 2.73
304 305 3.053619 TGACTGAGACCTAGCCACATCTA 60.054 47.826 0.00 0.00 0.00 1.98
306 307 2.103373 TGACTGAGACCTAGCCACATC 58.897 52.381 0.00 0.00 0.00 3.06
307 308 2.238084 TGACTGAGACCTAGCCACAT 57.762 50.000 0.00 0.00 0.00 3.21
361 362 3.820557 AGTCTCAGCCTTAAGTGCAAAA 58.179 40.909 15.45 3.17 0.00 2.44
364 365 4.283467 TCTTAAGTCTCAGCCTTAAGTGCA 59.717 41.667 13.61 0.00 45.93 4.57
411 412 7.064253 AGCGCTAATTTATTTTACGAGTCTTGT 59.936 33.333 8.99 0.00 0.00 3.16
412 413 7.399523 AGCGCTAATTTATTTTACGAGTCTTG 58.600 34.615 8.99 0.00 0.00 3.02
517 548 8.986991 ACTGAGTTGGAATGTTCTATCTTCTAT 58.013 33.333 0.00 0.00 0.00 1.98
519 550 7.251321 ACTGAGTTGGAATGTTCTATCTTCT 57.749 36.000 0.00 0.00 0.00 2.85
520 551 6.536941 GGACTGAGTTGGAATGTTCTATCTTC 59.463 42.308 0.00 0.00 0.00 2.87
522 553 5.394663 CGGACTGAGTTGGAATGTTCTATCT 60.395 44.000 0.00 0.00 0.00 1.98
523 554 4.806247 CGGACTGAGTTGGAATGTTCTATC 59.194 45.833 0.00 0.00 0.00 2.08
533 564 1.124780 TTTGACCGGACTGAGTTGGA 58.875 50.000 9.46 0.00 0.00 3.53
597 628 0.031585 AACAGCTGTGCTTCGTCGTA 59.968 50.000 22.49 0.00 36.40 3.43
700 732 2.753966 CCATCTGGTTCGGCGCAAG 61.754 63.158 10.83 1.95 43.44 4.01
717 749 3.675619 ATACGCGCCCAAGGTCACC 62.676 63.158 5.73 0.00 0.00 4.02
726 758 1.525077 TGGAATGGAATACGCGCCC 60.525 57.895 5.73 2.87 0.00 6.13
849 900 1.009675 CGCACAACACAAGCAGGAC 60.010 57.895 0.00 0.00 0.00 3.85
919 1020 0.693049 AAACTCTGCACCAGTAGGGG 59.307 55.000 0.00 0.00 42.91 4.79
920 1021 2.093447 CCTAAACTCTGCACCAGTAGGG 60.093 54.545 3.30 0.00 44.81 3.53
921 1022 2.832129 TCCTAAACTCTGCACCAGTAGG 59.168 50.000 4.41 4.41 42.21 3.18
922 1023 4.220821 TCTTCCTAAACTCTGCACCAGTAG 59.779 45.833 0.00 0.00 32.61 2.57
959 1060 2.434336 TGTACTCAAACTCTGCACCAGT 59.566 45.455 0.00 0.00 32.61 4.00
963 1064 2.739292 TCGTGTACTCAAACTCTGCAC 58.261 47.619 0.00 0.00 0.00 4.57
964 1065 3.067601 TCTTCGTGTACTCAAACTCTGCA 59.932 43.478 0.00 0.00 0.00 4.41
965 1066 3.639538 TCTTCGTGTACTCAAACTCTGC 58.360 45.455 0.00 0.00 0.00 4.26
966 1067 4.555360 CGATCTTCGTGTACTCAAACTCTG 59.445 45.833 0.00 0.00 34.72 3.35
967 1068 4.454847 TCGATCTTCGTGTACTCAAACTCT 59.545 41.667 0.00 0.00 41.35 3.24
968 1069 4.554200 GTCGATCTTCGTGTACTCAAACTC 59.446 45.833 0.00 0.00 41.35 3.01
969 1070 4.474113 GTCGATCTTCGTGTACTCAAACT 58.526 43.478 0.00 0.00 41.35 2.66
970 1071 3.607209 GGTCGATCTTCGTGTACTCAAAC 59.393 47.826 0.00 0.00 41.35 2.93
971 1072 3.253921 TGGTCGATCTTCGTGTACTCAAA 59.746 43.478 0.00 0.00 41.35 2.69
972 1073 2.815503 TGGTCGATCTTCGTGTACTCAA 59.184 45.455 0.00 0.00 41.35 3.02
973 1074 2.418976 CTGGTCGATCTTCGTGTACTCA 59.581 50.000 0.00 0.00 41.35 3.41
974 1075 2.419324 ACTGGTCGATCTTCGTGTACTC 59.581 50.000 0.00 0.00 41.35 2.59
975 1076 2.161808 CACTGGTCGATCTTCGTGTACT 59.838 50.000 0.00 0.00 41.35 2.73
976 1077 2.516923 CACTGGTCGATCTTCGTGTAC 58.483 52.381 0.00 0.00 41.35 2.90
978 1079 0.243907 CCACTGGTCGATCTTCGTGT 59.756 55.000 0.00 0.00 41.35 4.49
987 1088 1.114627 CCATCATCTCCACTGGTCGA 58.885 55.000 0.00 0.00 0.00 4.20
988 1089 0.531532 GCCATCATCTCCACTGGTCG 60.532 60.000 0.00 0.00 0.00 4.79
989 1090 0.543277 TGCCATCATCTCCACTGGTC 59.457 55.000 0.00 0.00 0.00 4.02
992 1093 0.179026 CCCTGCCATCATCTCCACTG 60.179 60.000 0.00 0.00 0.00 3.66
999 1100 1.228063 ACGATGCCCTGCCATCATC 60.228 57.895 0.00 0.00 41.27 2.92
1000 1101 1.527611 CACGATGCCCTGCCATCAT 60.528 57.895 0.00 0.00 41.27 2.45
1001 1102 2.124612 CACGATGCCCTGCCATCA 60.125 61.111 0.00 0.00 41.27 3.07
1056 1160 2.584835 TACCTGCAGGAATTGTTGCT 57.415 45.000 39.19 15.73 40.87 3.91
1057 1161 3.874392 ATTACCTGCAGGAATTGTTGC 57.126 42.857 39.19 4.26 40.67 4.17
1058 1162 4.220382 TGGAATTACCTGCAGGAATTGTTG 59.780 41.667 39.19 10.39 39.86 3.33
1059 1163 4.415596 TGGAATTACCTGCAGGAATTGTT 58.584 39.130 39.19 23.02 39.86 2.83
1060 1164 4.046286 TGGAATTACCTGCAGGAATTGT 57.954 40.909 39.19 18.87 39.86 2.71
1081 1188 5.940470 GCCCGATAAATAATCTGAAGTGGAT 59.060 40.000 0.00 0.00 31.87 3.41
1083 1190 4.152402 CGCCCGATAAATAATCTGAAGTGG 59.848 45.833 0.00 0.00 31.87 4.00
1085 1192 3.746492 GCGCCCGATAAATAATCTGAAGT 59.254 43.478 0.00 0.00 31.87 3.01
1097 1204 1.401761 TACCTAACTGCGCCCGATAA 58.598 50.000 4.18 0.00 0.00 1.75
1106 1213 1.128692 CTGCTTGCGTTACCTAACTGC 59.871 52.381 0.00 5.58 36.76 4.40
1107 1214 1.128692 GCTGCTTGCGTTACCTAACTG 59.871 52.381 0.00 0.00 34.12 3.16
1108 1215 1.439679 GCTGCTTGCGTTACCTAACT 58.560 50.000 0.00 0.00 34.12 2.24
1109 1216 3.969795 GCTGCTTGCGTTACCTAAC 57.030 52.632 0.00 0.00 0.00 2.34
1119 1226 1.710339 GCACGTACTAGCTGCTTGC 59.290 57.895 7.79 6.74 43.29 4.01
1120 1227 1.991430 CGCACGTACTAGCTGCTTG 59.009 57.895 7.79 8.80 0.00 4.01
1121 1228 1.805945 GCGCACGTACTAGCTGCTT 60.806 57.895 7.79 0.00 0.00 3.91
1122 1229 1.374343 TAGCGCACGTACTAGCTGCT 61.374 55.000 11.47 20.04 40.51 4.24
1123 1230 0.317938 ATAGCGCACGTACTAGCTGC 60.318 55.000 11.47 9.39 40.51 5.25
1124 1231 1.002792 TGATAGCGCACGTACTAGCTG 60.003 52.381 11.47 0.00 40.51 4.24
1125 1232 1.264557 CTGATAGCGCACGTACTAGCT 59.735 52.381 11.47 10.29 43.07 3.32
1126 1233 1.002684 ACTGATAGCGCACGTACTAGC 60.003 52.381 11.47 0.00 0.00 3.42
1127 1234 3.335786 AACTGATAGCGCACGTACTAG 57.664 47.619 11.47 0.56 0.00 2.57
1128 1235 4.787563 GCTTAACTGATAGCGCACGTACTA 60.788 45.833 11.47 0.00 0.00 1.82
1129 1236 3.692576 CTTAACTGATAGCGCACGTACT 58.307 45.455 11.47 0.00 0.00 2.73
1144 1251 7.122138 GGTTAGTACCCTATCTTGCTTAACT 57.878 40.000 0.00 0.00 38.60 2.24
1159 1266 1.022982 GCGCAACTGGGGTTAGTACC 61.023 60.000 0.30 0.00 44.22 3.34
1168 1275 4.025401 GTGGAACGCGCAACTGGG 62.025 66.667 5.73 0.00 0.00 4.45
1182 1289 3.047807 CGCTGTGTTTTTCCAACAGTGG 61.048 50.000 7.52 0.00 44.73 4.00
1260 1373 0.243907 GGTAGAGCTGCACGACTTCA 59.756 55.000 9.73 0.00 0.00 3.02
1341 1454 2.436646 CCGATGTTGGAGCCGCTT 60.437 61.111 0.00 0.00 0.00 4.68
1956 2096 5.630121 TGTTTGATCAGGTTCTGGTTGTAT 58.370 37.500 0.00 0.00 31.51 2.29
2240 2388 3.310774 AGCATGATGTTCGCATTCTACAC 59.689 43.478 0.00 0.00 38.08 2.90
2319 2471 4.026640 CGCTTTCGCCATCCAAATAATTTG 60.027 41.667 0.00 0.00 40.32 2.32
2320 2472 4.111916 CGCTTTCGCCATCCAAATAATTT 58.888 39.130 0.00 0.00 0.00 1.82
2321 2473 3.705604 CGCTTTCGCCATCCAAATAATT 58.294 40.909 0.00 0.00 0.00 1.40
2322 2474 3.354089 CGCTTTCGCCATCCAAATAAT 57.646 42.857 0.00 0.00 0.00 1.28
2323 2475 2.842208 CGCTTTCGCCATCCAAATAA 57.158 45.000 0.00 0.00 0.00 1.40
2357 2509 6.115446 CAGTGTGCCTCTTATTATTTCTCCA 58.885 40.000 0.00 0.00 0.00 3.86
2365 2520 3.712016 TTGCCAGTGTGCCTCTTATTA 57.288 42.857 1.78 0.00 0.00 0.98
2395 2550 6.478673 CGCCAAAAAGAAGTGGTAAAAGAAAT 59.521 34.615 0.00 0.00 37.23 2.17
2434 2589 4.571919 TCCAGTGAAATTACTACCCAACG 58.428 43.478 0.00 0.00 0.00 4.10
2443 2598 4.600062 AGGGGTTGATCCAGTGAAATTAC 58.400 43.478 0.00 0.00 38.11 1.89
2463 2618 1.038130 AGATCCGACGACAAGGGAGG 61.038 60.000 0.00 0.00 32.43 4.30
2472 2627 3.965292 GACTTATGTCAGATCCGACGA 57.035 47.619 4.66 0.00 42.48 4.20
2512 2668 4.661222 TGCATGTGGGAGTTTTCTATTGA 58.339 39.130 0.00 0.00 0.00 2.57
2536 2692 6.403866 TGTTGCCAACATACAAGAGAAATT 57.596 33.333 6.08 0.00 36.25 1.82
2631 2788 4.612264 ATTTTGCTGGTGAAAGATGCTT 57.388 36.364 0.00 0.00 0.00 3.91
2639 2796 5.278957 GCTTCTTCCTTATTTTGCTGGTGAA 60.279 40.000 0.00 0.00 0.00 3.18
2818 2975 1.342819 TGAAATTTGTTTCAGGGGCCG 59.657 47.619 0.00 0.00 36.15 6.13
2823 2980 7.486802 AAGAAGCAATGAAATTTGTTTCAGG 57.513 32.000 13.64 5.68 44.48 3.86
2837 2994 8.451687 TCGTTCAATGAAATAAAGAAGCAATG 57.548 30.769 0.00 0.00 0.00 2.82
2869 3026 7.375834 TGGTGAATTATGTACTCCGATGTATC 58.624 38.462 0.00 0.00 0.00 2.24
2876 3033 5.175859 ACAGTTGGTGAATTATGTACTCCG 58.824 41.667 0.00 0.00 0.00 4.63
2922 3079 8.514330 AGTGTCTAATTGTGGTTCTTGTTTTA 57.486 30.769 0.00 0.00 0.00 1.52
2962 3119 4.261801 ACTAGTGAAGCGGTTATGCAAAT 58.738 39.130 0.00 0.00 37.31 2.32
2963 3120 3.670625 ACTAGTGAAGCGGTTATGCAAA 58.329 40.909 0.00 0.00 37.31 3.68
2966 3123 2.351726 CCAACTAGTGAAGCGGTTATGC 59.648 50.000 0.00 0.00 0.00 3.14
2973 3130 9.651718 GAAAATATTAATCCAACTAGTGAAGCG 57.348 33.333 0.00 0.00 0.00 4.68
3000 3157 7.775093 TGAGGGAATTAACAATGAAGACATAGG 59.225 37.037 0.00 0.00 35.50 2.57
3012 3169 5.779771 AGAAGCCAATTGAGGGAATTAACAA 59.220 36.000 7.12 0.00 32.65 2.83
3033 3190 1.069204 AGAAGTGTGCAAGCTCGAGAA 59.931 47.619 18.75 0.00 0.00 2.87
3034 3191 0.676184 AGAAGTGTGCAAGCTCGAGA 59.324 50.000 18.75 0.00 0.00 4.04
3048 3205 5.277857 TCGGAACTGAAGAAGAAAGAAGT 57.722 39.130 0.00 0.00 0.00 3.01
3071 3228 0.850100 TGAGCCCCTCCTTTTGTTCA 59.150 50.000 0.00 0.00 0.00 3.18
3080 3237 2.127708 TCCTTATTCTTGAGCCCCTCC 58.872 52.381 0.00 0.00 0.00 4.30
3083 3240 2.234143 GCATCCTTATTCTTGAGCCCC 58.766 52.381 0.00 0.00 0.00 5.80
3085 3242 4.581824 TCATTGCATCCTTATTCTTGAGCC 59.418 41.667 0.00 0.00 0.00 4.70
3101 3258 6.602410 TCCTTGTTCCATTTTATCATTGCA 57.398 33.333 0.00 0.00 0.00 4.08
3102 3259 8.392612 CAATTCCTTGTTCCATTTTATCATTGC 58.607 33.333 0.00 0.00 0.00 3.56
3105 3262 7.567458 CCCAATTCCTTGTTCCATTTTATCAT 58.433 34.615 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.