Multiple sequence alignment - TraesCS3D01G116300

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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 TraesCS3D01G116300 chr3D 100.000 3391 0 0 1 3391 69793377 69796767 0.000000e+00 6263.0
1 TraesCS3D01G116300 chr3A 92.424 2323 131 28 1094 3391 81095297 81097599 0.000000e+00 3273.0
2 TraesCS3D01G116300 chr3A 85.790 1126 81 43 1 1092 81094272 81095352 0.000000e+00 1120.0
3 TraesCS3D01G116300 chr3B 92.297 2103 117 26 1318 3391 115553839 115555925 0.000000e+00 2944.0
4 TraesCS3D01G116300 chr3B 91.564 569 29 8 758 1326 115553124 115553673 0.000000e+00 767.0
5 TraesCS3D01G116300 chr3B 74.143 700 76 52 17 623 115552337 115553024 3.450000e-45 193.0
6 TraesCS3D01G116300 chr3B 100.000 32 0 0 592 623 115553076 115553107 3.650000e-05 60.2
7 TraesCS3D01G116300 chr7B 89.903 515 48 3 1276 1788 709579753 709579241 0.000000e+00 660.0


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 TraesCS3D01G116300 chr3D 69793377 69796767 3390 False 6263.00 6263 100.000 1 3391 1 chr3D.!!$F1 3390
1 TraesCS3D01G116300 chr3A 81094272 81097599 3327 False 2196.50 3273 89.107 1 3391 2 chr3A.!!$F1 3390
2 TraesCS3D01G116300 chr3B 115552337 115555925 3588 False 991.05 2944 89.501 17 3391 4 chr3B.!!$F1 3374
3 TraesCS3D01G116300 chr7B 709579241 709579753 512 True 660.00 660 89.903 1276 1788 1 chr7B.!!$R1 512

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
177 208 0.043334 TCTTCTTCTCCCCTCCCCTG 59.957 60.0 0.0 0.0 0.00 4.45 F
444 524 0.109086 CCGATTCGTCTGTCTGCTGT 60.109 55.0 5.2 0.0 0.00 4.40 F
660 771 0.178950 TCTCCTGAGTCCAGTGTGCT 60.179 55.0 0.0 0.0 38.74 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2533 0.040958 GGAACAACACTTGCTGCGAG 60.041 55.000 15.31 15.31 0.0 5.03 R
2158 2536 3.004734 ACATTAGGAACAACACTTGCTGC 59.995 43.478 0.00 0.00 0.0 5.25 R
2463 2842 5.777802 ACGATCTGCTATCCTCAACATTAG 58.222 41.667 0.00 0.00 0.0 1.73 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
22 23 1.262950 TCGACCGCAAACAAGTCATTG 59.737 47.619 0.00 0.00 42.46 2.82
59 61 3.866582 GCCCTGGGGTCTCCATCG 61.867 72.222 16.03 0.00 46.01 3.84
60 62 2.365635 CCCTGGGGTCTCCATCGT 60.366 66.667 4.27 0.00 46.01 3.73
61 63 2.435693 CCCTGGGGTCTCCATCGTC 61.436 68.421 4.27 0.00 46.01 4.20
62 64 1.381872 CCTGGGGTCTCCATCGTCT 60.382 63.158 0.00 0.00 46.01 4.18
64 66 1.680522 CTGGGGTCTCCATCGTCTGG 61.681 65.000 0.00 0.98 46.01 3.86
67 69 2.060980 GGTCTCCATCGTCTGGCCT 61.061 63.158 3.32 0.00 45.52 5.19
69 71 2.060383 TCTCCATCGTCTGGCCTGG 61.060 63.158 10.07 4.85 45.52 4.45
167 198 2.094957 CCTCGTGTCCACTCTTCTTCTC 60.095 54.545 0.00 0.00 0.00 2.87
169 200 1.067495 CGTGTCCACTCTTCTTCTCCC 60.067 57.143 0.00 0.00 0.00 4.30
171 202 1.150135 TGTCCACTCTTCTTCTCCCCT 59.850 52.381 0.00 0.00 0.00 4.79
175 206 0.043485 ACTCTTCTTCTCCCCTCCCC 59.957 60.000 0.00 0.00 0.00 4.81
176 207 0.341609 CTCTTCTTCTCCCCTCCCCT 59.658 60.000 0.00 0.00 0.00 4.79
177 208 0.043334 TCTTCTTCTCCCCTCCCCTG 59.957 60.000 0.00 0.00 0.00 4.45
178 209 1.616628 TTCTTCTCCCCTCCCCTGC 60.617 63.158 0.00 0.00 0.00 4.85
214 260 4.097361 GTGTTCTCCCCTCCCGGC 62.097 72.222 0.00 0.00 0.00 6.13
229 275 3.483869 GGCCTCATCCGCCCTTCT 61.484 66.667 0.00 0.00 40.78 2.85
334 388 5.490995 GGAACCCTATCCTATCCTATCCT 57.509 47.826 0.00 0.00 36.50 3.24
335 389 6.609379 GGAACCCTATCCTATCCTATCCTA 57.391 45.833 0.00 0.00 36.50 2.94
336 390 7.182017 GGAACCCTATCCTATCCTATCCTAT 57.818 44.000 0.00 0.00 36.50 2.57
337 391 8.303338 GGAACCCTATCCTATCCTATCCTATA 57.697 42.308 0.00 0.00 36.50 1.31
338 392 8.172070 GGAACCCTATCCTATCCTATCCTATAC 58.828 44.444 0.00 0.00 36.50 1.47
346 400 5.775701 CCTATCCTATCCTATACCGATTGGG 59.224 48.000 3.39 0.00 40.75 4.12
357 411 1.967319 CCGATTGGGTTATCTGGGTG 58.033 55.000 0.00 0.00 0.00 4.61
358 412 1.476833 CCGATTGGGTTATCTGGGTGG 60.477 57.143 0.00 0.00 0.00 4.61
359 413 1.488812 CGATTGGGTTATCTGGGTGGA 59.511 52.381 0.00 0.00 0.00 4.02
360 414 2.106511 CGATTGGGTTATCTGGGTGGAT 59.893 50.000 0.00 0.00 0.00 3.41
380 460 3.312736 TTCCCTTCTTCCTTTTGCTGT 57.687 42.857 0.00 0.00 0.00 4.40
444 524 0.109086 CCGATTCGTCTGTCTGCTGT 60.109 55.000 5.20 0.00 0.00 4.40
493 590 0.898320 TTGTCTGGTCTGGCTAGCTC 59.102 55.000 15.72 5.44 0.00 4.09
580 691 9.483916 TGAATTCGTCTAGATTTGTTTGTTCTA 57.516 29.630 0.00 0.00 0.00 2.10
636 747 7.559590 AGCAACAAGAATAGCTCGAAATTAT 57.440 32.000 0.00 0.00 30.05 1.28
659 770 0.246086 CTCTCCTGAGTCCAGTGTGC 59.754 60.000 0.00 0.00 38.74 4.57
660 771 0.178950 TCTCCTGAGTCCAGTGTGCT 60.179 55.000 0.00 0.00 38.74 4.40
678 795 1.202417 GCTGCCGACTTCTGTATGCTA 60.202 52.381 0.00 0.00 0.00 3.49
769 886 2.064434 TGCTCACAACATTTGTCCCA 57.936 45.000 0.00 0.00 43.23 4.37
788 905 5.030147 TCCCAACCAACTAGACTGATATGT 58.970 41.667 0.00 0.00 0.00 2.29
802 919 5.660460 ACTGATATGTGCGTTCATACAGAA 58.340 37.500 21.53 0.00 35.55 3.02
806 923 7.408910 TGATATGTGCGTTCATACAGAAATTG 58.591 34.615 4.39 0.00 38.13 2.32
836 953 8.590204 TGTATATATAATTTTCTCTCCGGTGCA 58.410 33.333 0.00 0.00 0.00 4.57
842 959 1.471829 TTCTCTCCGGTGCAGCAAGA 61.472 55.000 17.33 15.94 0.00 3.02
858 975 1.667724 CAAGATGACCATTCTGACGCC 59.332 52.381 0.00 0.00 0.00 5.68
859 976 0.904649 AGATGACCATTCTGACGCCA 59.095 50.000 0.00 0.00 0.00 5.69
860 977 1.487976 AGATGACCATTCTGACGCCAT 59.512 47.619 0.00 0.00 0.00 4.40
911 1028 4.995487 ACTGTTCTGTTTTATTCCTCGGAC 59.005 41.667 0.00 0.00 0.00 4.79
1048 1222 6.867662 ACCTTGTATCTGTCTTTTGAGTTG 57.132 37.500 0.00 0.00 0.00 3.16
1070 1244 4.399934 TGAACTTAAGTTTTCCTTTGCCGT 59.600 37.500 21.40 0.00 38.56 5.68
1077 1251 3.435671 AGTTTTCCTTTGCCGTTAGATCG 59.564 43.478 0.00 0.00 0.00 3.69
1078 1252 1.365699 TTCCTTTGCCGTTAGATCGC 58.634 50.000 0.00 0.00 0.00 4.58
1079 1253 0.535335 TCCTTTGCCGTTAGATCGCT 59.465 50.000 0.00 0.00 0.00 4.93
1080 1254 1.066430 TCCTTTGCCGTTAGATCGCTT 60.066 47.619 0.00 0.00 0.00 4.68
1081 1255 2.166870 TCCTTTGCCGTTAGATCGCTTA 59.833 45.455 0.00 0.00 0.00 3.09
1082 1256 2.284417 CCTTTGCCGTTAGATCGCTTAC 59.716 50.000 0.00 0.00 0.00 2.34
1083 1257 1.552226 TTGCCGTTAGATCGCTTACG 58.448 50.000 0.00 0.00 44.28 3.18
1084 1258 0.452987 TGCCGTTAGATCGCTTACGT 59.547 50.000 0.00 0.00 43.45 3.57
1085 1259 1.135315 TGCCGTTAGATCGCTTACGTT 60.135 47.619 0.00 0.00 43.45 3.99
1086 1260 2.097304 TGCCGTTAGATCGCTTACGTTA 59.903 45.455 0.00 0.00 43.45 3.18
1087 1261 3.243168 TGCCGTTAGATCGCTTACGTTAT 60.243 43.478 0.00 0.00 43.45 1.89
1088 1262 3.119136 GCCGTTAGATCGCTTACGTTATG 59.881 47.826 0.00 0.00 43.45 1.90
1089 1263 3.119136 CCGTTAGATCGCTTACGTTATGC 59.881 47.826 0.00 0.00 43.45 3.14
1090 1264 3.727227 CGTTAGATCGCTTACGTTATGCA 59.273 43.478 0.00 0.00 40.96 3.96
1091 1265 4.143803 CGTTAGATCGCTTACGTTATGCAG 60.144 45.833 0.00 0.00 40.96 4.41
1092 1266 2.743938 AGATCGCTTACGTTATGCAGG 58.256 47.619 0.00 0.00 41.18 4.85
1093 1267 2.361119 AGATCGCTTACGTTATGCAGGA 59.639 45.455 0.00 0.00 41.18 3.86
1094 1268 2.882927 TCGCTTACGTTATGCAGGAT 57.117 45.000 0.00 0.00 41.18 3.24
1095 1269 2.739292 TCGCTTACGTTATGCAGGATC 58.261 47.619 0.00 0.00 41.18 3.36
1096 1270 2.361119 TCGCTTACGTTATGCAGGATCT 59.639 45.455 0.00 0.00 41.18 2.75
1097 1271 3.123804 CGCTTACGTTATGCAGGATCTT 58.876 45.455 0.00 0.00 33.53 2.40
1098 1272 3.555956 CGCTTACGTTATGCAGGATCTTT 59.444 43.478 0.00 0.00 33.53 2.52
1099 1273 4.034048 CGCTTACGTTATGCAGGATCTTTT 59.966 41.667 0.00 0.00 33.53 2.27
1100 1274 5.266242 GCTTACGTTATGCAGGATCTTTTG 58.734 41.667 0.00 0.00 0.00 2.44
1101 1275 5.064707 GCTTACGTTATGCAGGATCTTTTGA 59.935 40.000 0.00 0.00 0.00 2.69
1102 1276 6.662414 TTACGTTATGCAGGATCTTTTGAG 57.338 37.500 0.00 0.00 0.00 3.02
1103 1277 4.579869 ACGTTATGCAGGATCTTTTGAGT 58.420 39.130 0.00 0.00 0.00 3.41
1104 1278 5.003804 ACGTTATGCAGGATCTTTTGAGTT 58.996 37.500 0.00 0.00 0.00 3.01
1105 1279 5.122396 ACGTTATGCAGGATCTTTTGAGTTC 59.878 40.000 0.00 0.00 0.00 3.01
1106 1280 5.122239 CGTTATGCAGGATCTTTTGAGTTCA 59.878 40.000 0.00 0.00 0.00 3.18
1107 1281 6.348458 CGTTATGCAGGATCTTTTGAGTTCAA 60.348 38.462 0.00 0.00 0.00 2.69
1108 1282 7.370383 GTTATGCAGGATCTTTTGAGTTCAAA 58.630 34.615 3.28 3.28 43.36 2.69
1109 1283 6.600882 ATGCAGGATCTTTTGAGTTCAAAT 57.399 33.333 8.02 0.00 44.30 2.32
1110 1284 6.409524 TGCAGGATCTTTTGAGTTCAAATT 57.590 33.333 8.02 0.00 44.30 1.82
1111 1285 7.523293 TGCAGGATCTTTTGAGTTCAAATTA 57.477 32.000 8.02 1.05 44.30 1.40
1112 1286 7.950512 TGCAGGATCTTTTGAGTTCAAATTAA 58.049 30.769 8.02 0.00 44.30 1.40
1113 1287 8.084073 TGCAGGATCTTTTGAGTTCAAATTAAG 58.916 33.333 8.02 3.85 44.30 1.85
1114 1288 8.299570 GCAGGATCTTTTGAGTTCAAATTAAGA 58.700 33.333 8.02 8.54 44.30 2.10
1124 1298 8.816640 TGAGTTCAAATTAAGATTTCCTTTGC 57.183 30.769 0.00 0.00 36.34 3.68
1125 1299 7.872483 TGAGTTCAAATTAAGATTTCCTTTGCC 59.128 33.333 0.00 0.00 36.34 4.52
1126 1300 6.868339 AGTTCAAATTAAGATTTCCTTTGCCG 59.132 34.615 0.00 0.00 36.34 5.69
1127 1301 5.167845 TCAAATTAAGATTTCCTTTGCCGC 58.832 37.500 0.00 0.00 36.34 6.53
1128 1302 5.047377 TCAAATTAAGATTTCCTTTGCCGCT 60.047 36.000 0.00 0.00 36.34 5.52
1129 1303 6.151985 TCAAATTAAGATTTCCTTTGCCGCTA 59.848 34.615 0.00 0.00 36.34 4.26
1130 1304 5.757850 ATTAAGATTTCCTTTGCCGCTAG 57.242 39.130 0.00 0.00 36.34 3.42
1131 1305 3.350219 AAGATTTCCTTTGCCGCTAGA 57.650 42.857 0.00 0.00 0.00 2.43
1132 1306 3.567478 AGATTTCCTTTGCCGCTAGAT 57.433 42.857 0.00 0.00 0.00 1.98
1133 1307 3.471680 AGATTTCCTTTGCCGCTAGATC 58.528 45.455 0.00 0.00 0.00 2.75
1175 1349 5.153950 ACAGAACCCTTAGTCTGTCATTC 57.846 43.478 0.53 0.00 38.92 2.67
1218 1406 4.746535 ACATGATGTTGACATACCGGTA 57.253 40.909 18.46 18.46 36.57 4.02
1225 1413 5.347620 TGTTGACATACCGGTATTTAGCT 57.652 39.130 24.71 0.06 0.00 3.32
1227 1415 5.583061 TGTTGACATACCGGTATTTAGCTTG 59.417 40.000 24.71 15.26 0.00 4.01
1228 1416 5.601583 TGACATACCGGTATTTAGCTTGA 57.398 39.130 24.71 0.00 0.00 3.02
1230 1418 6.220930 TGACATACCGGTATTTAGCTTGATC 58.779 40.000 24.71 12.65 0.00 2.92
1231 1419 6.169557 ACATACCGGTATTTAGCTTGATCA 57.830 37.500 24.71 0.00 0.00 2.92
1232 1420 6.769512 ACATACCGGTATTTAGCTTGATCAT 58.230 36.000 24.71 0.00 0.00 2.45
1233 1421 7.903145 ACATACCGGTATTTAGCTTGATCATA 58.097 34.615 24.71 0.00 0.00 2.15
1234 1422 7.817962 ACATACCGGTATTTAGCTTGATCATAC 59.182 37.037 24.71 0.00 0.00 2.39
1235 1423 5.548406 ACCGGTATTTAGCTTGATCATACC 58.452 41.667 4.49 8.71 37.20 2.73
1238 1426 5.548406 GGTATTTAGCTTGATCATACCGGT 58.452 41.667 13.98 13.98 32.22 5.28
1239 1427 5.638234 GGTATTTAGCTTGATCATACCGGTC 59.362 44.000 12.40 0.00 32.22 4.79
1240 1428 5.552870 ATTTAGCTTGATCATACCGGTCT 57.447 39.130 12.40 0.00 0.00 3.85
1241 1429 5.353394 TTTAGCTTGATCATACCGGTCTT 57.647 39.130 12.40 0.00 0.00 3.01
1242 1430 3.914426 AGCTTGATCATACCGGTCTTT 57.086 42.857 12.40 0.00 0.00 2.52
1243 1431 6.474140 TTAGCTTGATCATACCGGTCTTTA 57.526 37.500 12.40 0.00 0.00 1.85
1244 1432 4.950050 AGCTTGATCATACCGGTCTTTAG 58.050 43.478 12.40 1.77 0.00 1.85
1245 1433 3.495001 GCTTGATCATACCGGTCTTTAGC 59.505 47.826 12.40 8.77 0.00 3.09
1249 1437 6.413783 TGATCATACCGGTCTTTAGCATAA 57.586 37.500 12.40 0.00 0.00 1.90
1484 1847 2.235898 AGATGAAGAGAACCCACAGCTC 59.764 50.000 0.00 0.00 0.00 4.09
1520 1883 0.752658 GCCTTCCTTGCTTTGGTTGT 59.247 50.000 0.00 0.00 0.00 3.32
1560 1923 3.560636 AAGAATCCCTTACCATCCACG 57.439 47.619 0.00 0.00 32.24 4.94
1875 2241 6.693113 CAGAAAGCAAAAGAGTTTTCCTGTAC 59.307 38.462 0.00 0.00 38.86 2.90
1921 2287 4.508551 ACCATCATGCAACCTGATTAGA 57.491 40.909 0.00 0.00 31.00 2.10
1993 2371 3.886505 TGTGTTTTAATCCCGTTTGCTCT 59.113 39.130 0.00 0.00 0.00 4.09
2135 2513 5.288472 GTGTGCAGTCCTTTTAACAGTTTTG 59.712 40.000 0.00 0.00 0.00 2.44
2155 2533 5.570234 TTGTACCTTGACAAACTTGTTCC 57.430 39.130 0.00 0.00 42.43 3.62
2158 2536 2.943033 ACCTTGACAAACTTGTTCCTCG 59.057 45.455 0.00 0.00 42.43 4.63
2163 2541 0.662619 CAAACTTGTTCCTCGCAGCA 59.337 50.000 0.00 0.00 0.00 4.41
2169 2547 0.463654 TGTTCCTCGCAGCAAGTGTT 60.464 50.000 0.00 0.00 0.00 3.32
2230 2609 4.622740 GGCAACTCTTTACATCATTTGCAC 59.377 41.667 5.83 0.00 39.67 4.57
2372 2751 6.776887 ATTACCCTCTCCATCATTCTGATT 57.223 37.500 0.00 0.00 34.28 2.57
2726 3111 6.183360 GCTGGGATTGAAACTGTAGTCATTAC 60.183 42.308 0.00 0.00 0.00 1.89
2729 3114 6.316390 GGGATTGAAACTGTAGTCATTACCAG 59.684 42.308 10.48 0.00 31.19 4.00
2748 3136 2.171237 CAGCAACTCACCATGGGAGATA 59.829 50.000 27.34 5.64 36.26 1.98
2775 3163 6.174720 TGATACACCTGGAAGTCATTATCC 57.825 41.667 0.00 0.00 36.21 2.59
2790 3178 3.909776 TTATCCAGTATAGCACCGTCG 57.090 47.619 0.00 0.00 0.00 5.12
2796 3184 1.941294 AGTATAGCACCGTCGTCTGAG 59.059 52.381 0.00 0.00 0.00 3.35
2819 3207 5.409826 AGCTTGTCGAATTCTTAAGAGGTTG 59.590 40.000 5.12 2.26 0.00 3.77
2851 3239 2.040679 ACACCTATTTTAGTTGCGGGGT 59.959 45.455 0.00 0.00 0.00 4.95
2853 3241 1.404035 CCTATTTTAGTTGCGGGGTGC 59.596 52.381 0.00 0.00 46.70 5.01
2900 3288 6.127026 GGTAGTACCAAGTCAAATGAGGATCT 60.127 42.308 14.82 0.00 38.42 2.75
2905 3293 7.205515 ACCAAGTCAAATGAGGATCTAGATT 57.794 36.000 6.70 0.00 34.92 2.40
2934 3324 4.482684 TCGAGAGCGCGCTTCAGG 62.483 66.667 36.87 23.44 37.46 3.86
2962 3357 2.525368 TCCGTCTCTCCAGTTGATTCA 58.475 47.619 0.00 0.00 0.00 2.57
2964 3359 3.323691 TCCGTCTCTCCAGTTGATTCAAA 59.676 43.478 0.00 0.00 0.00 2.69
2972 3367 4.630111 TCCAGTTGATTCAAATGTTTGGC 58.370 39.130 21.40 0.00 37.68 4.52
2983 3378 6.757897 TCAAATGTTTGGCTATAGAGTTGG 57.242 37.500 3.21 0.00 38.66 3.77
3030 3425 7.886338 AGGATGAATTTTCTGGTTACAGTTTC 58.114 34.615 0.00 0.00 45.14 2.78
3033 3428 9.528018 GATGAATTTTCTGGTTACAGTTTCAAA 57.472 29.630 0.00 0.00 45.14 2.69
3034 3429 8.925161 TGAATTTTCTGGTTACAGTTTCAAAG 57.075 30.769 0.00 0.00 45.14 2.77
3035 3430 8.527810 TGAATTTTCTGGTTACAGTTTCAAAGT 58.472 29.630 0.00 0.00 45.14 2.66
3048 3444 5.009210 CAGTTTCAAAGTAACCGGGATTTCA 59.991 40.000 6.32 0.00 0.00 2.69
3061 3457 4.450757 CCGGGATTTCATTTTCCAAAACAC 59.549 41.667 0.00 0.00 33.43 3.32
3072 3468 0.030638 CCAAAACACCTGGCACTTCG 59.969 55.000 0.00 0.00 0.00 3.79
3085 3481 3.197766 TGGCACTTCGTTATTCCAGAGAT 59.802 43.478 0.00 0.00 0.00 2.75
3094 3490 8.818141 TTCGTTATTCCAGAGATTCATCATAC 57.182 34.615 0.00 0.00 0.00 2.39
3115 3511 2.393271 AAGTTTGAGGGATGAGCTCG 57.607 50.000 9.64 0.00 0.00 5.03
3118 3514 0.617535 TTTGAGGGATGAGCTCGGGA 60.618 55.000 9.64 0.00 0.00 5.14
3138 3534 2.622942 GAGCAACACCATGGAAAACAGA 59.377 45.455 21.47 0.00 0.00 3.41
3179 3575 1.663695 GCCCTAGCTAAAACATGCGA 58.336 50.000 0.00 0.00 35.50 5.10
3180 3576 1.330829 GCCCTAGCTAAAACATGCGAC 59.669 52.381 0.00 0.00 35.50 5.19
3198 3594 2.673833 GACGCCTTATTCGTATCAGGG 58.326 52.381 4.64 0.00 40.59 4.45
3256 3652 0.391661 AGCGCCTCAATGTCGAACAT 60.392 50.000 2.29 0.00 41.31 2.71
3294 3690 7.112565 CGCATTTGAACATATCTGATAAAGTGC 59.887 37.037 12.67 12.67 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.002900 ACGGACAATGACTTGTTTGCG 60.003 47.619 0.00 0.00 45.57 4.85
8 9 2.384382 CACGGACAATGACTTGTTTGC 58.616 47.619 0.00 0.00 45.57 3.68
10 11 2.650322 ACCACGGACAATGACTTGTTT 58.350 42.857 0.00 0.00 45.57 2.83
14 15 5.221165 CCTTTTTAACCACGGACAATGACTT 60.221 40.000 0.00 0.00 0.00 3.01
15 16 4.277423 CCTTTTTAACCACGGACAATGACT 59.723 41.667 0.00 0.00 0.00 3.41
22 23 0.599558 GGCCCTTTTTAACCACGGAC 59.400 55.000 0.00 0.00 0.00 4.79
59 61 0.179062 CTATGTGAGCCAGGCCAGAC 60.179 60.000 8.22 2.71 0.00 3.51
60 62 1.976132 GCTATGTGAGCCAGGCCAGA 61.976 60.000 8.22 4.93 46.41 3.86
61 63 1.525535 GCTATGTGAGCCAGGCCAG 60.526 63.158 8.22 0.00 46.41 4.85
62 64 2.591753 GCTATGTGAGCCAGGCCA 59.408 61.111 8.22 2.73 46.41 5.36
119 133 2.676342 GCCCGTAGTATTTGTGTGGAAG 59.324 50.000 0.00 0.00 0.00 3.46
178 209 4.806339 AGAAGGGGCGAGAGGGGG 62.806 72.222 0.00 0.00 0.00 5.40
190 221 0.615850 GAGGGGAGAACACCAGAAGG 59.384 60.000 0.00 0.00 43.15 3.46
214 260 0.105778 GAAGAGAAGGGCGGATGAGG 59.894 60.000 0.00 0.00 0.00 3.86
218 264 1.051556 GGGAGAAGAGAAGGGCGGAT 61.052 60.000 0.00 0.00 0.00 4.18
277 328 1.817099 GAAGCCGATCCAGCACCAG 60.817 63.158 5.28 0.00 0.00 4.00
278 329 1.841302 AAGAAGCCGATCCAGCACCA 61.841 55.000 5.28 0.00 0.00 4.17
279 330 1.078143 AAGAAGCCGATCCAGCACC 60.078 57.895 5.28 0.00 0.00 5.01
325 379 5.222278 ACCCAATCGGTATAGGATAGGAT 57.778 43.478 8.57 0.00 45.97 3.24
338 392 1.476833 CCACCCAGATAACCCAATCGG 60.477 57.143 0.00 0.00 37.81 4.18
355 409 3.056536 GCAAAAGGAAGAAGGGAATCCAC 60.057 47.826 0.09 0.00 35.62 4.02
357 411 3.194329 CAGCAAAAGGAAGAAGGGAATCC 59.806 47.826 0.00 0.00 0.00 3.01
358 412 3.829026 ACAGCAAAAGGAAGAAGGGAATC 59.171 43.478 0.00 0.00 0.00 2.52
359 413 3.575687 CACAGCAAAAGGAAGAAGGGAAT 59.424 43.478 0.00 0.00 0.00 3.01
360 414 2.958355 CACAGCAAAAGGAAGAAGGGAA 59.042 45.455 0.00 0.00 0.00 3.97
397 477 1.815421 CGACGGGGATTCAGGCTTG 60.815 63.158 0.00 0.00 0.00 4.01
444 524 0.107831 GCACCAACCAGTCTACCACA 59.892 55.000 0.00 0.00 0.00 4.17
580 691 9.275398 CTCTAATACTCCAACTCTCGTTAGTAT 57.725 37.037 0.00 0.00 36.88 2.12
651 762 2.281070 AAGTCGGCAGCACACTGG 60.281 61.111 0.00 0.00 44.63 4.00
655 766 0.608130 ATACAGAAGTCGGCAGCACA 59.392 50.000 0.00 0.00 0.00 4.57
656 767 1.002366 CATACAGAAGTCGGCAGCAC 58.998 55.000 0.00 0.00 0.00 4.40
657 768 0.740868 GCATACAGAAGTCGGCAGCA 60.741 55.000 0.00 0.00 0.00 4.41
658 769 0.460987 AGCATACAGAAGTCGGCAGC 60.461 55.000 0.00 0.00 31.50 5.25
659 770 2.871182 TAGCATACAGAAGTCGGCAG 57.129 50.000 0.00 0.00 31.50 4.85
660 771 3.118775 ACATTAGCATACAGAAGTCGGCA 60.119 43.478 0.00 0.00 31.50 5.69
678 795 4.761227 GCCATGTCCAAAATTCCAAACATT 59.239 37.500 0.00 0.00 0.00 2.71
769 886 4.081642 ACGCACATATCAGTCTAGTTGGTT 60.082 41.667 0.00 0.00 0.00 3.67
788 905 4.700268 ATGCAATTTCTGTATGAACGCA 57.300 36.364 0.00 0.00 38.27 5.24
832 949 2.089980 AGAATGGTCATCTTGCTGCAC 58.910 47.619 0.00 0.00 0.00 4.57
836 953 2.625737 CGTCAGAATGGTCATCTTGCT 58.374 47.619 0.00 0.00 36.16 3.91
842 959 2.424601 CAAATGGCGTCAGAATGGTCAT 59.575 45.455 0.00 0.00 36.16 3.06
858 975 4.126208 TGGCACATAAATCCTGCAAATG 57.874 40.909 0.00 0.00 32.20 2.32
859 976 4.761975 CTTGGCACATAAATCCTGCAAAT 58.238 39.130 0.00 0.00 39.30 2.32
860 977 3.617045 GCTTGGCACATAAATCCTGCAAA 60.617 43.478 0.00 0.00 39.30 3.68
911 1028 3.318839 TGGAATCAGCTCAACAAGTTTGG 59.681 43.478 0.00 0.00 0.00 3.28
1048 1222 4.928601 ACGGCAAAGGAAAACTTAAGTTC 58.071 39.130 20.78 9.82 38.85 3.01
1070 1244 4.037089 TCCTGCATAACGTAAGCGATCTAA 59.963 41.667 0.00 0.00 45.62 2.10
1077 1251 5.064707 TCAAAAGATCCTGCATAACGTAAGC 59.935 40.000 0.00 0.00 45.62 3.09
1079 1253 6.170506 ACTCAAAAGATCCTGCATAACGTAA 58.829 36.000 0.00 0.00 0.00 3.18
1080 1254 5.730550 ACTCAAAAGATCCTGCATAACGTA 58.269 37.500 0.00 0.00 0.00 3.57
1081 1255 4.579869 ACTCAAAAGATCCTGCATAACGT 58.420 39.130 0.00 0.00 0.00 3.99
1082 1256 5.122239 TGAACTCAAAAGATCCTGCATAACG 59.878 40.000 0.00 0.00 0.00 3.18
1083 1257 6.500684 TGAACTCAAAAGATCCTGCATAAC 57.499 37.500 0.00 0.00 0.00 1.89
1084 1258 7.523293 TTTGAACTCAAAAGATCCTGCATAA 57.477 32.000 2.38 0.00 42.26 1.90
1098 1272 9.260002 GCAAAGGAAATCTTAATTTGAACTCAA 57.740 29.630 0.00 0.00 35.21 3.02
1099 1273 7.872483 GGCAAAGGAAATCTTAATTTGAACTCA 59.128 33.333 0.00 0.00 35.21 3.41
1100 1274 7.062255 CGGCAAAGGAAATCTTAATTTGAACTC 59.938 37.037 0.00 0.00 35.21 3.01
1101 1275 6.868339 CGGCAAAGGAAATCTTAATTTGAACT 59.132 34.615 0.00 0.00 35.21 3.01
1102 1276 6.401047 GCGGCAAAGGAAATCTTAATTTGAAC 60.401 38.462 0.00 0.00 35.21 3.18
1103 1277 5.637387 GCGGCAAAGGAAATCTTAATTTGAA 59.363 36.000 0.00 0.00 35.21 2.69
1104 1278 5.047377 AGCGGCAAAGGAAATCTTAATTTGA 60.047 36.000 1.45 0.00 35.21 2.69
1105 1279 5.170748 AGCGGCAAAGGAAATCTTAATTTG 58.829 37.500 1.45 0.00 35.21 2.32
1106 1280 5.405935 AGCGGCAAAGGAAATCTTAATTT 57.594 34.783 1.45 0.00 37.80 1.82
1107 1281 5.885912 TCTAGCGGCAAAGGAAATCTTAATT 59.114 36.000 1.45 0.00 34.78 1.40
1108 1282 5.437060 TCTAGCGGCAAAGGAAATCTTAAT 58.563 37.500 1.45 0.00 34.78 1.40
1109 1283 4.839121 TCTAGCGGCAAAGGAAATCTTAA 58.161 39.130 1.45 0.00 34.78 1.85
1110 1284 4.481368 TCTAGCGGCAAAGGAAATCTTA 57.519 40.909 1.45 0.00 34.78 2.10
1111 1285 3.350219 TCTAGCGGCAAAGGAAATCTT 57.650 42.857 1.45 0.00 37.28 2.40
1112 1286 3.471680 GATCTAGCGGCAAAGGAAATCT 58.528 45.455 1.45 0.00 0.00 2.40
1113 1287 2.221981 CGATCTAGCGGCAAAGGAAATC 59.778 50.000 1.45 0.00 0.00 2.17
1114 1288 2.213499 CGATCTAGCGGCAAAGGAAAT 58.787 47.619 1.45 0.00 0.00 2.17
1115 1289 1.651987 CGATCTAGCGGCAAAGGAAA 58.348 50.000 1.45 0.00 0.00 3.13
1116 1290 0.810031 GCGATCTAGCGGCAAAGGAA 60.810 55.000 1.45 0.00 0.00 3.36
1117 1291 1.227263 GCGATCTAGCGGCAAAGGA 60.227 57.895 1.45 0.00 0.00 3.36
1118 1292 0.811616 AAGCGATCTAGCGGCAAAGG 60.812 55.000 1.45 0.00 43.00 3.11
1119 1293 1.523095 GTAAGCGATCTAGCGGCAAAG 59.477 52.381 1.45 0.00 43.00 2.77
1120 1294 1.567504 GTAAGCGATCTAGCGGCAAA 58.432 50.000 1.45 0.00 43.00 3.68
1121 1295 0.594028 CGTAAGCGATCTAGCGGCAA 60.594 55.000 1.45 0.00 43.00 4.52
1122 1296 1.008881 CGTAAGCGATCTAGCGGCA 60.009 57.895 1.45 0.00 43.00 5.69
1123 1297 0.594284 AACGTAAGCGATCTAGCGGC 60.594 55.000 0.00 0.00 43.00 6.53
1124 1298 2.675767 TAACGTAAGCGATCTAGCGG 57.324 50.000 0.00 0.00 43.00 5.52
1125 1299 2.338813 GCATAACGTAAGCGATCTAGCG 59.661 50.000 0.00 0.00 43.00 4.26
1126 1300 3.305964 TGCATAACGTAAGCGATCTAGC 58.694 45.455 0.00 0.00 45.62 3.42
1127 1301 3.914966 CCTGCATAACGTAAGCGATCTAG 59.085 47.826 0.00 0.00 45.62 2.43
1128 1302 3.566742 TCCTGCATAACGTAAGCGATCTA 59.433 43.478 0.00 0.00 45.62 1.98
1129 1303 2.361119 TCCTGCATAACGTAAGCGATCT 59.639 45.455 0.00 0.00 45.62 2.75
1130 1304 2.726760 CTCCTGCATAACGTAAGCGATC 59.273 50.000 0.00 0.00 45.62 3.69
1131 1305 2.361119 TCTCCTGCATAACGTAAGCGAT 59.639 45.455 0.00 0.00 45.62 4.58
1132 1306 1.746787 TCTCCTGCATAACGTAAGCGA 59.253 47.619 0.00 0.00 45.62 4.93
1133 1307 2.203800 TCTCCTGCATAACGTAAGCG 57.796 50.000 0.00 0.00 45.62 4.68
1189 1377 9.855021 CGGTATGTCAACATCATGTAATAGATA 57.145 33.333 0.00 0.00 37.76 1.98
1218 1406 5.552870 AGACCGGTATGATCAAGCTAAAT 57.447 39.130 7.34 0.00 0.00 1.40
1225 1413 4.746535 TGCTAAAGACCGGTATGATCAA 57.253 40.909 7.34 0.00 0.00 2.57
1227 1415 8.251721 ACTATTATGCTAAAGACCGGTATGATC 58.748 37.037 7.34 0.00 0.00 2.92
1228 1416 8.035394 CACTATTATGCTAAAGACCGGTATGAT 58.965 37.037 7.34 0.00 0.00 2.45
1230 1418 7.152645 ACACTATTATGCTAAAGACCGGTATG 58.847 38.462 7.34 0.00 0.00 2.39
1231 1419 7.299246 ACACTATTATGCTAAAGACCGGTAT 57.701 36.000 7.34 0.00 0.00 2.73
1232 1420 6.720112 ACACTATTATGCTAAAGACCGGTA 57.280 37.500 7.34 0.00 0.00 4.02
1233 1421 5.609533 ACACTATTATGCTAAAGACCGGT 57.390 39.130 6.92 6.92 0.00 5.28
1234 1422 9.701098 TTTATACACTATTATGCTAAAGACCGG 57.299 33.333 0.00 0.00 0.00 5.28
1242 1430 9.353999 CGCTGATGTTTATACACTATTATGCTA 57.646 33.333 0.00 0.00 37.03 3.49
1243 1431 8.088365 TCGCTGATGTTTATACACTATTATGCT 58.912 33.333 0.00 0.00 37.03 3.79
1244 1432 8.239681 TCGCTGATGTTTATACACTATTATGC 57.760 34.615 0.00 0.00 37.03 3.14
1245 1433 9.626045 TCTCGCTGATGTTTATACACTATTATG 57.374 33.333 0.00 0.00 37.03 1.90
1306 1494 5.201243 AGCTAAAGCCCTAATAAACAAGGG 58.799 41.667 2.90 2.90 43.38 3.95
1484 1847 0.110644 GGCGTCTCTCAAACTTTGCG 60.111 55.000 0.00 0.00 0.00 4.85
1560 1923 6.704512 TTTGAAAACTGAACTGAAGTTTGC 57.295 33.333 2.56 1.68 44.93 3.68
1788 2153 9.956720 CATCTATGAGTTGTTTTCTTTCAAGTT 57.043 29.630 0.00 0.00 0.00 2.66
1875 2241 8.430063 GTTTACATGCATGAAGAAATGACTTTG 58.570 33.333 32.75 2.21 0.00 2.77
1921 2287 4.516698 GTGACAGAACCATCAACACATCTT 59.483 41.667 0.00 0.00 0.00 2.40
2135 2513 4.025145 CGAGGAACAAGTTTGTCAAGGTAC 60.025 45.833 0.00 0.00 41.31 3.34
2155 2533 0.040958 GGAACAACACTTGCTGCGAG 60.041 55.000 15.31 15.31 0.00 5.03
2158 2536 3.004734 ACATTAGGAACAACACTTGCTGC 59.995 43.478 0.00 0.00 0.00 5.25
2163 2541 7.404671 AACTGAAACATTAGGAACAACACTT 57.595 32.000 0.00 0.00 0.00 3.16
2169 2547 9.616156 TGTTTAGTAACTGAAACATTAGGAACA 57.384 29.630 0.00 0.00 39.88 3.18
2230 2609 7.390162 AGCTTATCAGGACAGAAGAAGAAAAAG 59.610 37.037 0.00 0.00 0.00 2.27
2463 2842 5.777802 ACGATCTGCTATCCTCAACATTAG 58.222 41.667 0.00 0.00 0.00 1.73
2473 2852 6.701841 TGATGAACTAAAACGATCTGCTATCC 59.298 38.462 0.00 0.00 0.00 2.59
2726 3111 0.679002 CTCCCATGGTGAGTTGCTGG 60.679 60.000 11.73 0.00 0.00 4.85
2729 3114 2.092968 TGTATCTCCCATGGTGAGTTGC 60.093 50.000 22.26 18.86 0.00 4.17
2748 3136 3.239449 TGACTTCCAGGTGTATCAGTGT 58.761 45.455 0.00 0.00 0.00 3.55
2775 3163 1.669265 TCAGACGACGGTGCTATACTG 59.331 52.381 0.00 0.00 41.64 2.74
2790 3178 5.864474 TCTTAAGAATTCGACAAGCTCAGAC 59.136 40.000 1.68 0.00 0.00 3.51
2796 3184 5.408604 TCAACCTCTTAAGAATTCGACAAGC 59.591 40.000 6.63 0.00 0.00 4.01
2832 3220 2.718563 CACCCCGCAACTAAAATAGGT 58.281 47.619 0.00 0.00 0.00 3.08
2851 3239 1.261480 AAAACCCACACAACACTGCA 58.739 45.000 0.00 0.00 0.00 4.41
2853 3241 3.584406 TGAAAAACCCACACAACACTG 57.416 42.857 0.00 0.00 0.00 3.66
2854 3242 3.118811 CCATGAAAAACCCACACAACACT 60.119 43.478 0.00 0.00 0.00 3.55
2855 3243 3.194062 CCATGAAAAACCCACACAACAC 58.806 45.455 0.00 0.00 0.00 3.32
2859 3247 3.904717 ACTACCATGAAAAACCCACACA 58.095 40.909 0.00 0.00 0.00 3.72
2860 3248 4.216902 GGTACTACCATGAAAAACCCACAC 59.783 45.833 0.00 0.00 38.42 3.82
2861 3249 4.141228 TGGTACTACCATGAAAAACCCACA 60.141 41.667 3.57 0.00 44.79 4.17
2885 3273 7.125507 ACACTCAATCTAGATCCTCATTTGACT 59.874 37.037 5.51 0.00 0.00 3.41
2888 3276 7.767659 TGAACACTCAATCTAGATCCTCATTTG 59.232 37.037 5.51 0.00 0.00 2.32
2890 3278 7.429374 TGAACACTCAATCTAGATCCTCATT 57.571 36.000 5.51 0.00 0.00 2.57
2892 3280 6.838090 AGATGAACACTCAATCTAGATCCTCA 59.162 38.462 5.51 2.42 34.49 3.86
2895 3283 6.016693 TCGAGATGAACACTCAATCTAGATCC 60.017 42.308 5.51 0.00 34.49 3.36
2900 3288 5.220951 GCTCTCGAGATGAACACTCAATCTA 60.221 44.000 17.03 0.00 34.49 1.98
2905 3293 1.131315 CGCTCTCGAGATGAACACTCA 59.869 52.381 17.03 0.00 38.10 3.41
2934 3324 1.330655 TGGAGAGACGGAATGGCTCC 61.331 60.000 0.00 0.00 44.18 4.70
2962 3357 7.539034 AAACCAACTCTATAGCCAAACATTT 57.461 32.000 0.00 0.00 0.00 2.32
2964 3359 7.285401 CCATAAACCAACTCTATAGCCAAACAT 59.715 37.037 0.00 0.00 0.00 2.71
2972 3367 6.480320 GTCTGTGCCATAAACCAACTCTATAG 59.520 42.308 0.00 0.00 0.00 1.31
2983 3378 3.146066 TGAACAGGTCTGTGCCATAAAC 58.854 45.455 4.22 0.00 44.13 2.01
2997 3392 5.244626 ACCAGAAAATTCATCCTTGAACAGG 59.755 40.000 0.00 0.00 44.36 4.00
3030 3425 5.867174 GGAAAATGAAATCCCGGTTACTTTG 59.133 40.000 0.00 0.00 0.00 2.77
3033 3428 4.668636 TGGAAAATGAAATCCCGGTTACT 58.331 39.130 0.00 0.00 34.68 2.24
3034 3429 5.394224 TTGGAAAATGAAATCCCGGTTAC 57.606 39.130 0.00 0.00 34.68 2.50
3035 3430 6.183360 TGTTTTGGAAAATGAAATCCCGGTTA 60.183 34.615 0.00 0.00 34.68 2.85
3036 3431 4.965200 TTTGGAAAATGAAATCCCGGTT 57.035 36.364 0.00 0.00 34.68 4.44
3048 3444 2.771372 AGTGCCAGGTGTTTTGGAAAAT 59.229 40.909 0.00 0.00 37.96 1.82
3061 3457 2.009774 CTGGAATAACGAAGTGCCAGG 58.990 52.381 0.00 0.00 45.00 4.45
3085 3481 7.174413 TCATCCCTCAAACTTTGTATGATGAA 58.826 34.615 19.05 10.44 36.66 2.57
3094 3490 2.417933 CGAGCTCATCCCTCAAACTTTG 59.582 50.000 15.40 0.00 0.00 2.77
3115 3511 1.000843 GTTTTCCATGGTGTTGCTCCC 59.999 52.381 12.58 0.00 0.00 4.30
3118 3514 2.665165 TCTGTTTTCCATGGTGTTGCT 58.335 42.857 12.58 0.00 0.00 3.91
3148 3544 1.621672 GCTAGGGCTGGTGAGCTTCT 61.622 60.000 0.00 0.00 45.44 2.85
3160 3556 1.330829 GTCGCATGTTTTAGCTAGGGC 59.669 52.381 0.00 0.00 39.06 5.19
3179 3575 1.343465 CCCCTGATACGAATAAGGCGT 59.657 52.381 0.00 0.00 45.01 5.68
3180 3576 1.337823 CCCCCTGATACGAATAAGGCG 60.338 57.143 0.00 0.00 32.65 5.52
3198 3594 3.953612 TCTGCATATTTCAACCATGTCCC 59.046 43.478 0.00 0.00 0.00 4.46
3256 3652 6.006759 TGTTCAAATGCGAATGTTGTATCA 57.993 33.333 0.00 0.00 0.00 2.15
3311 3707 3.756117 ACTGAAAAGTCCTTGGATCACC 58.244 45.455 0.00 0.00 0.00 4.02
3318 3714 7.274250 GCATAGCAATTTACTGAAAAGTCCTTG 59.726 37.037 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.