Multiple sequence alignment - TraesCS1D01G003800

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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 TraesCS1D01G003800 chr1D 100.000 3266 0 0 1 3266 2073834 2077099 0.000000e+00 6032
1 TraesCS1D01G003800 chr1B 90.728 2114 98 41 1205 3266 1201706 1203773 0.000000e+00 2728
2 TraesCS1D01G003800 chr1B 79.752 242 30 11 332 567 1200986 1201214 1.210000e-34 158
3 TraesCS1D01G003800 chr1B 95.652 92 4 0 1075 1166 1201607 1201698 7.300000e-32 148
4 TraesCS1D01G003800 chr1A 90.926 1587 86 27 1592 3145 1157617 1159178 0.000000e+00 2080
5 TraesCS1D01G003800 chr1A 77.399 792 97 58 622 1378 1156866 1157610 2.360000e-106 396
6 TraesCS1D01G003800 chr1A 79.856 417 50 8 1 393 1156000 1156406 1.150000e-69 274
7 TraesCS1D01G003800 chr7B 89.307 851 49 17 2163 2995 493170637 493171463 0.000000e+00 1029
8 TraesCS1D01G003800 chr7B 78.324 346 55 7 1 327 249679062 249679406 4.270000e-49 206
9 TraesCS1D01G003800 chr6B 91.379 232 15 3 2765 2995 663954039 663953812 2.450000e-81 313
10 TraesCS1D01G003800 chr4B 93.252 163 10 1 2834 2995 654929648 654929486 4.210000e-59 239
11 TraesCS1D01G003800 chr4B 93.252 163 10 1 2834 2995 654969993 654969831 4.210000e-59 239
12 TraesCS1D01G003800 chr4B 93.252 163 10 1 2834 2995 655005118 655004956 4.210000e-59 239
13 TraesCS1D01G003800 chr4B 93.252 163 10 1 2834 2995 655040857 655040695 4.210000e-59 239
14 TraesCS1D01G003800 chr7D 77.493 351 59 6 1 331 268569604 268569954 3.330000e-45 193
15 TraesCS1D01G003800 chr7A 76.353 351 62 8 1 331 294564025 294564374 5.600000e-38 169


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 TraesCS1D01G003800 chr1D 2073834 2077099 3265 False 6032.000000 6032 100.000000 1 3266 1 chr1D.!!$F1 3265
1 TraesCS1D01G003800 chr1B 1200986 1203773 2787 False 1011.333333 2728 88.710667 332 3266 3 chr1B.!!$F1 2934
2 TraesCS1D01G003800 chr1A 1156000 1159178 3178 False 916.666667 2080 82.727000 1 3145 3 chr1A.!!$F1 3144
3 TraesCS1D01G003800 chr7B 493170637 493171463 826 False 1029.000000 1029 89.307000 2163 2995 1 chr7B.!!$F2 832

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
846 1215 0.179051 CGTAGGAGCGAGGAGGTACT 60.179 60.0 0.0 0.0 45.03 2.73 F
1458 1903 0.032678 CGGGTCAGCATCGCTCTAAT 59.967 55.0 0.0 0.0 36.40 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 2194 0.179076 CGATGATGCTGCTGTGGGTA 60.179 55.0 0.00 0.00 0.00 3.69 R
2636 3131 0.730840 TTAGAAGCTCGATCGTCGCA 59.269 50.0 25.44 9.33 40.21 5.10 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 4.457603 AGATCAAGGACGAGGAAGATATCG 59.542 45.833 0.00 0.00 44.36 2.92
61 62 2.753452 GGACGAGGAAGATATCGCCATA 59.247 50.000 16.72 0.00 42.61 2.74
63 64 2.492484 ACGAGGAAGATATCGCCATACC 59.508 50.000 16.72 7.33 42.61 2.73
65 66 2.168728 GAGGAAGATATCGCCATACCCC 59.831 54.545 16.72 3.60 0.00 4.95
66 67 1.134788 GGAAGATATCGCCATACCCCG 60.135 57.143 11.43 0.00 0.00 5.73
67 68 1.549170 GAAGATATCGCCATACCCCGT 59.451 52.381 0.00 0.00 0.00 5.28
68 69 1.183549 AGATATCGCCATACCCCGTC 58.816 55.000 0.00 0.00 0.00 4.79
69 70 0.179145 GATATCGCCATACCCCGTCG 60.179 60.000 0.00 0.00 0.00 5.12
70 71 2.221906 ATATCGCCATACCCCGTCGC 62.222 60.000 0.00 0.00 0.00 5.19
74 75 2.522436 CCATACCCCGTCGCCCTA 60.522 66.667 0.00 0.00 0.00 3.53
97 105 1.388547 GGCGGTAATGAAGCAATGGA 58.611 50.000 0.00 0.00 0.00 3.41
113 121 0.322456 TGGATGGTTTTGAGGCCTCG 60.322 55.000 27.43 0.00 0.00 4.63
132 140 1.153765 TTGCGTCATGAGGCTCTCG 60.154 57.895 33.17 17.30 42.21 4.04
165 186 2.145225 CGAGTCCAGAACTTGCACG 58.855 57.895 0.00 0.00 38.74 5.34
168 189 0.753262 AGTCCAGAACTTGCACGAGT 59.247 50.000 0.00 0.00 33.03 4.18
175 196 0.951040 AACTTGCACGAGTAGCTGGC 60.951 55.000 0.00 0.00 0.00 4.85
203 224 1.203174 AGGGGCTGGCAATACTTTTGT 60.203 47.619 2.88 0.00 0.00 2.83
207 228 1.882198 CTGGCAATACTTTTGTCGCG 58.118 50.000 0.00 0.00 0.00 5.87
210 231 1.733360 GGCAATACTTTTGTCGCGGTA 59.267 47.619 6.13 0.00 0.00 4.02
214 235 4.391358 CAATACTTTTGTCGCGGTAACAG 58.609 43.478 6.13 7.05 0.00 3.16
216 237 1.202557 ACTTTTGTCGCGGTAACAGGA 60.203 47.619 6.13 0.00 0.00 3.86
222 243 1.588139 CGCGGTAACAGGATCGTCC 60.588 63.158 0.00 0.00 36.58 4.79
224 245 1.673808 GCGGTAACAGGATCGTCCCT 61.674 60.000 1.06 0.00 37.19 4.20
239 261 2.360980 CCTGGGACCTCCTCGTCT 59.639 66.667 0.00 0.00 36.20 4.18
241 263 1.608717 CCTGGGACCTCCTCGTCTTG 61.609 65.000 0.00 0.00 36.20 3.02
249 271 2.202676 CCTCGTCTTGCGGCTCTC 60.203 66.667 0.00 0.00 41.72 3.20
252 274 2.048222 CGTCTTGCGGCTCTCCAA 60.048 61.111 0.00 0.00 36.85 3.53
266 288 0.321122 CTCCAAGCTCGGCTTCAAGT 60.321 55.000 7.99 0.00 46.77 3.16
273 295 1.301677 CTCGGCTTCAAGTTCCAGGC 61.302 60.000 0.00 0.00 0.00 4.85
276 298 0.328258 GGCTTCAAGTTCCAGGCCTA 59.672 55.000 3.98 0.00 36.96 3.93
286 308 1.675641 CCAGGCCTACAACACCAGC 60.676 63.158 3.98 0.00 0.00 4.85
299 321 1.523258 ACCAGCAGCTCGATCATGC 60.523 57.895 8.20 8.20 40.29 4.06
306 328 2.176273 GCTCGATCATGCGCAAGGT 61.176 57.895 17.11 5.94 38.28 3.50
311 333 2.056481 GATCATGCGCAAGGTGAGGC 62.056 60.000 17.11 6.78 38.28 4.70
330 352 1.003355 GCCAGAAGCACTGCTACCA 60.003 57.895 3.33 0.00 44.52 3.25
366 392 0.605860 CATCCAGCATGCCCTCTAGC 60.606 60.000 15.66 0.00 31.97 3.42
380 408 1.272490 CTCTAGCTGGTCGGTTTGTCA 59.728 52.381 0.00 0.00 0.00 3.58
399 428 4.478195 CCGTCTGATGTCGGTGAC 57.522 61.111 0.00 0.00 39.42 3.67
401 430 1.584495 CGTCTGATGTCGGTGACCA 59.416 57.895 1.11 0.00 0.00 4.02
413 442 5.067273 TGTCGGTGACCATTTGAACTTTAT 58.933 37.500 1.11 0.00 0.00 1.40
420 449 5.710099 TGACCATTTGAACTTTATCTGGGTC 59.290 40.000 0.00 0.00 41.02 4.46
423 452 5.480073 CCATTTGAACTTTATCTGGGTCCAA 59.520 40.000 0.00 0.00 0.00 3.53
425 454 4.715534 TGAACTTTATCTGGGTCCAACA 57.284 40.909 0.00 0.00 0.00 3.33
426 455 4.394729 TGAACTTTATCTGGGTCCAACAC 58.605 43.478 0.00 0.00 0.00 3.32
471 699 2.029623 GATGCCCATGCTGTCTTGAAT 58.970 47.619 0.00 0.00 38.71 2.57
478 706 4.365723 CCATGCTGTCTTGAATTTATGCC 58.634 43.478 0.00 0.00 0.00 4.40
479 707 4.365723 CATGCTGTCTTGAATTTATGCCC 58.634 43.478 0.00 0.00 0.00 5.36
483 711 5.893255 TGCTGTCTTGAATTTATGCCCTTAT 59.107 36.000 0.00 0.00 0.00 1.73
487 718 6.096705 TGTCTTGAATTTATGCCCTTATGTGG 59.903 38.462 0.00 0.00 0.00 4.17
493 724 2.425143 ATGCCCTTATGTGGTGTCTG 57.575 50.000 0.00 0.00 0.00 3.51
502 733 2.779755 TGTGGTGTCTGTTGTGAAGT 57.220 45.000 0.00 0.00 0.00 3.01
530 767 4.081406 TCTTATGTGACCTGCTGCATTTT 58.919 39.130 1.31 0.00 0.00 1.82
538 775 1.164411 CTGCTGCATTTTCGGTGGTA 58.836 50.000 1.31 0.00 0.00 3.25
541 778 1.810151 GCTGCATTTTCGGTGGTAAGA 59.190 47.619 0.00 0.00 0.00 2.10
582 841 3.574614 GGTGAGCAAAATAACACGCAAT 58.425 40.909 0.00 0.00 34.59 3.56
587 846 5.925397 TGAGCAAAATAACACGCAATCAAAT 59.075 32.000 0.00 0.00 0.00 2.32
592 851 8.167985 GCAAAATAACACGCAATCAAATAACAT 58.832 29.630 0.00 0.00 0.00 2.71
599 858 4.458989 ACGCAATCAAATAACATCTGTGGT 59.541 37.500 0.00 0.00 0.00 4.16
611 870 0.463654 TCTGTGGTTTGCGTCTGCTT 60.464 50.000 0.00 0.00 43.34 3.91
613 872 1.806542 CTGTGGTTTGCGTCTGCTTAT 59.193 47.619 0.00 0.00 43.34 1.73
615 874 1.804151 GTGGTTTGCGTCTGCTTATCA 59.196 47.619 0.00 0.00 43.34 2.15
617 876 1.130561 GGTTTGCGTCTGCTTATCACC 59.869 52.381 0.00 0.00 43.34 4.02
630 982 3.246226 GCTTATCACCGTACAATGCAGAG 59.754 47.826 0.00 0.00 0.00 3.35
641 993 4.045636 ACAATGCAGAGAACCAAACAAC 57.954 40.909 0.00 0.00 0.00 3.32
645 997 6.015180 ACAATGCAGAGAACCAAACAACATAT 60.015 34.615 0.00 0.00 0.00 1.78
646 998 5.375417 TGCAGAGAACCAAACAACATATG 57.625 39.130 0.00 0.00 0.00 1.78
693 1046 3.935993 GCTCAACCAGCCTCAACTA 57.064 52.632 0.00 0.00 43.17 2.24
694 1047 1.731720 GCTCAACCAGCCTCAACTAG 58.268 55.000 0.00 0.00 43.17 2.57
708 1061 5.317733 CTCAACTAGGAGGACAACTAGTG 57.682 47.826 0.00 0.00 46.70 2.74
709 1062 4.737578 TCAACTAGGAGGACAACTAGTGT 58.262 43.478 0.00 0.00 46.70 3.55
710 1063 5.884322 TCAACTAGGAGGACAACTAGTGTA 58.116 41.667 0.00 0.00 46.70 2.90
711 1064 5.944599 TCAACTAGGAGGACAACTAGTGTAG 59.055 44.000 0.00 0.00 46.70 2.74
712 1065 4.857679 ACTAGGAGGACAACTAGTGTAGG 58.142 47.826 0.00 0.00 45.91 3.18
713 1066 3.103080 AGGAGGACAACTAGTGTAGGG 57.897 52.381 0.00 0.00 41.96 3.53
714 1067 1.481363 GGAGGACAACTAGTGTAGGGC 59.519 57.143 0.00 0.00 41.96 5.19
715 1068 1.481363 GAGGACAACTAGTGTAGGGCC 59.519 57.143 0.00 0.00 41.96 5.80
716 1069 1.203262 AGGACAACTAGTGTAGGGCCA 60.203 52.381 6.18 0.00 41.96 5.36
717 1070 1.066358 GGACAACTAGTGTAGGGCCAC 60.066 57.143 6.18 2.35 41.96 5.01
718 1071 1.621814 GACAACTAGTGTAGGGCCACA 59.378 52.381 6.18 5.41 41.96 4.17
719 1072 2.236395 GACAACTAGTGTAGGGCCACAT 59.764 50.000 6.18 0.00 41.96 3.21
720 1073 2.642807 ACAACTAGTGTAGGGCCACATT 59.357 45.455 6.18 7.78 39.29 2.71
721 1074 3.009723 CAACTAGTGTAGGGCCACATTG 58.990 50.000 6.18 6.11 37.82 2.82
722 1075 2.546899 ACTAGTGTAGGGCCACATTGA 58.453 47.619 6.18 0.00 37.82 2.57
723 1076 3.115390 ACTAGTGTAGGGCCACATTGAT 58.885 45.455 6.18 0.00 37.82 2.57
724 1077 2.717639 AGTGTAGGGCCACATTGATC 57.282 50.000 6.18 0.00 37.82 2.92
725 1078 1.134401 AGTGTAGGGCCACATTGATCG 60.134 52.381 6.18 0.00 37.82 3.69
726 1079 1.134521 GTGTAGGGCCACATTGATCGA 60.135 52.381 6.18 0.00 35.38 3.59
727 1080 1.138859 TGTAGGGCCACATTGATCGAG 59.861 52.381 6.18 0.00 0.00 4.04
728 1081 0.758734 TAGGGCCACATTGATCGAGG 59.241 55.000 6.18 0.00 0.00 4.63
729 1082 1.526917 GGGCCACATTGATCGAGGG 60.527 63.158 4.39 0.00 0.00 4.30
730 1083 1.526887 GGCCACATTGATCGAGGGA 59.473 57.895 0.00 0.00 0.00 4.20
731 1084 0.533755 GGCCACATTGATCGAGGGAG 60.534 60.000 0.00 0.00 0.00 4.30
732 1085 0.533755 GCCACATTGATCGAGGGAGG 60.534 60.000 0.00 2.08 0.00 4.30
739 1092 1.153349 GATCGAGGGAGGGTGTTGC 60.153 63.158 0.00 0.00 0.00 4.17
809 1178 2.938956 AAAGTTGTGACTGAGGAGGG 57.061 50.000 0.00 0.00 35.91 4.30
815 1184 2.680352 GACTGAGGAGGGGCACGA 60.680 66.667 0.00 0.00 0.00 4.35
831 1200 2.659291 GCACGAAAAGAGTTGCACGTAG 60.659 50.000 0.00 0.00 32.89 3.51
835 1204 1.797025 AAAGAGTTGCACGTAGGAGC 58.203 50.000 0.00 0.00 0.00 4.70
837 1206 1.211969 GAGTTGCACGTAGGAGCGA 59.788 57.895 0.00 0.00 35.46 4.93
838 1207 0.798771 GAGTTGCACGTAGGAGCGAG 60.799 60.000 0.00 0.00 35.46 5.03
839 1208 1.805945 GTTGCACGTAGGAGCGAGG 60.806 63.158 0.00 0.00 35.46 4.63
840 1209 1.974875 TTGCACGTAGGAGCGAGGA 60.975 57.895 0.00 0.00 35.46 3.71
841 1210 1.934220 TTGCACGTAGGAGCGAGGAG 61.934 60.000 0.00 0.00 35.46 3.69
842 1211 3.111939 CACGTAGGAGCGAGGAGG 58.888 66.667 0.00 0.00 35.59 4.30
843 1212 1.749638 CACGTAGGAGCGAGGAGGT 60.750 63.158 0.00 0.00 35.59 3.85
844 1213 0.463295 CACGTAGGAGCGAGGAGGTA 60.463 60.000 0.00 0.00 35.59 3.08
845 1214 0.463474 ACGTAGGAGCGAGGAGGTAC 60.463 60.000 0.00 0.00 35.59 3.34
846 1215 0.179051 CGTAGGAGCGAGGAGGTACT 60.179 60.000 0.00 0.00 45.03 2.73
847 1216 4.691547 ACGTAGGAGCGAGGAGGTACTC 62.692 59.091 0.00 0.00 41.42 2.59
866 1235 2.357517 CACGTGGAGTGGAGGCAC 60.358 66.667 7.95 0.00 46.77 5.01
867 1236 2.872388 CACGTGGAGTGGAGGCACT 61.872 63.158 7.95 0.00 46.77 4.40
896 1279 4.364686 TCCCCACTTCCCCTCCCC 62.365 72.222 0.00 0.00 0.00 4.81
898 1281 2.204306 CCCACTTCCCCTCCCCTT 60.204 66.667 0.00 0.00 0.00 3.95
899 1282 2.309504 CCCACTTCCCCTCCCCTTC 61.310 68.421 0.00 0.00 0.00 3.46
901 1284 0.846870 CCACTTCCCCTCCCCTTCTT 60.847 60.000 0.00 0.00 0.00 2.52
902 1285 0.621082 CACTTCCCCTCCCCTTCTTC 59.379 60.000 0.00 0.00 0.00 2.87
903 1286 0.498685 ACTTCCCCTCCCCTTCTTCT 59.501 55.000 0.00 0.00 0.00 2.85
906 1289 2.066999 CCCCTCCCCTTCTTCTCCG 61.067 68.421 0.00 0.00 0.00 4.63
908 1291 2.736826 CCTCCCCTTCTTCTCCGCC 61.737 68.421 0.00 0.00 0.00 6.13
909 1292 3.075005 TCCCCTTCTTCTCCGCCG 61.075 66.667 0.00 0.00 0.00 6.46
910 1293 4.840005 CCCCTTCTTCTCCGCCGC 62.840 72.222 0.00 0.00 0.00 6.53
911 1294 3.775654 CCCTTCTTCTCCGCCGCT 61.776 66.667 0.00 0.00 0.00 5.52
912 1295 2.202810 CCTTCTTCTCCGCCGCTC 60.203 66.667 0.00 0.00 0.00 5.03
913 1296 2.202810 CTTCTTCTCCGCCGCTCC 60.203 66.667 0.00 0.00 0.00 4.70
929 1312 3.130819 CCGCCAGCATTAACCGCA 61.131 61.111 1.88 0.00 0.00 5.69
1134 1555 1.066858 AGGTACCTCGACGACTACGAA 60.067 52.381 9.21 0.00 42.66 3.85
1136 1557 2.352960 GGTACCTCGACGACTACGAAAT 59.647 50.000 4.06 0.00 42.66 2.17
1312 1748 2.331805 CCGCATCTCCCTACGACG 59.668 66.667 0.00 0.00 0.00 5.12
1323 1759 3.770353 CTACGACGACGAGCCGCTC 62.770 68.421 15.32 10.59 42.66 5.03
1434 1876 1.151450 CAAGGACACTGCCCTGGTT 59.849 57.895 0.00 0.00 33.55 3.67
1436 1878 0.400594 AAGGACACTGCCCTGGTTAC 59.599 55.000 0.00 0.00 33.55 2.50
1440 1885 1.671054 CACTGCCCTGGTTACCACG 60.671 63.158 0.00 0.00 0.00 4.94
1458 1903 0.032678 CGGGTCAGCATCGCTCTAAT 59.967 55.000 0.00 0.00 36.40 1.73
1461 1906 2.289320 GGGTCAGCATCGCTCTAATGAT 60.289 50.000 0.00 0.00 36.40 2.45
1653 2113 0.035915 GACCCAGCAAGAGGAGGAAC 60.036 60.000 0.00 0.00 0.00 3.62
1665 2128 4.753186 AGAGGAGGAACAAGAAGAAGGTA 58.247 43.478 0.00 0.00 0.00 3.08
1680 2143 0.981183 AGGTAACATTCGCACTGGGA 59.019 50.000 0.00 0.00 41.41 4.37
1742 2208 3.080641 TGCTACCCACAGCAGCAT 58.919 55.556 0.00 0.00 46.41 3.79
1745 2211 0.465097 GCTACCCACAGCAGCATCAT 60.465 55.000 0.00 0.00 41.40 2.45
2210 2676 1.458777 TGGTCAAGGTCGACAGGGT 60.459 57.895 18.91 0.00 37.66 4.34
2290 2756 3.824810 GCTTGGATCAGCTCTGCC 58.175 61.111 0.00 0.00 36.79 4.85
2291 2757 1.224039 GCTTGGATCAGCTCTGCCT 59.776 57.895 0.00 0.00 36.79 4.75
2292 2758 0.814812 GCTTGGATCAGCTCTGCCTC 60.815 60.000 0.00 0.00 36.79 4.70
2293 2759 0.540454 CTTGGATCAGCTCTGCCTCA 59.460 55.000 0.00 0.00 0.00 3.86
2294 2760 0.540454 TTGGATCAGCTCTGCCTCAG 59.460 55.000 0.00 0.00 0.00 3.35
2295 2761 1.227615 GGATCAGCTCTGCCTCAGC 60.228 63.158 0.00 0.00 40.48 4.26
2298 2768 0.976590 ATCAGCTCTGCCTCAGCTCA 60.977 55.000 0.00 0.00 44.25 4.26
2339 2812 6.215227 GCTCTCCCTACCTCCTAGTATAGTTA 59.785 46.154 0.00 0.00 36.82 2.24
2340 2813 7.256980 GCTCTCCCTACCTCCTAGTATAGTTAA 60.257 44.444 0.00 0.00 36.82 2.01
2341 2814 8.217188 TCTCCCTACCTCCTAGTATAGTTAAG 57.783 42.308 0.00 0.00 36.82 1.85
2503 2988 8.346828 ACCCCCTAGTATAGTTAGTTTAGTCAA 58.653 37.037 0.00 0.00 36.82 3.18
2636 3131 2.510238 GGCTGCAGCGACGATCTT 60.510 61.111 31.19 0.00 43.26 2.40
2641 3136 2.990735 CAGCGACGATCTTGCGAC 59.009 61.111 0.00 0.00 33.89 5.19
2774 3278 6.092092 TGATGATAAAATGCAGTTGGTTTCG 58.908 36.000 0.00 0.00 0.00 3.46
3089 3598 3.636300 TGCACAACAGAATACCAAAAGCT 59.364 39.130 0.00 0.00 0.00 3.74
3093 3602 4.452455 ACAACAGAATACCAAAAGCTCTCG 59.548 41.667 0.00 0.00 0.00 4.04
3153 3666 6.601217 TGCATTATAGCTCACAACCATAACAA 59.399 34.615 0.00 0.00 34.99 2.83
3187 3703 6.202762 TGTTTTTCAGTGTACAGCAGATAGTG 59.797 38.462 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.175760 TGAACCATAGTGGCTCTCGC 59.824 55.000 0.00 0.00 42.67 5.03
16 17 2.831685 TCTGCACGTTGAACCATAGT 57.168 45.000 0.00 0.00 0.00 2.12
20 21 1.872952 CTTGATCTGCACGTTGAACCA 59.127 47.619 0.00 0.00 0.00 3.67
71 72 1.810412 GCTTCATTACCGCCCTGTAGG 60.810 57.143 0.00 0.00 39.47 3.18
73 74 0.906066 TGCTTCATTACCGCCCTGTA 59.094 50.000 0.00 0.00 0.00 2.74
74 75 0.037590 TTGCTTCATTACCGCCCTGT 59.962 50.000 0.00 0.00 0.00 4.00
78 86 1.388547 TCCATTGCTTCATTACCGCC 58.611 50.000 0.00 0.00 0.00 6.13
82 90 6.397272 TCAAAACCATCCATTGCTTCATTAC 58.603 36.000 0.00 0.00 0.00 1.89
86 94 3.258872 CCTCAAAACCATCCATTGCTTCA 59.741 43.478 0.00 0.00 0.00 3.02
97 105 1.247567 CAACGAGGCCTCAAAACCAT 58.752 50.000 31.67 6.80 0.00 3.55
102 110 1.959226 GACGCAACGAGGCCTCAAA 60.959 57.895 31.67 0.00 0.00 2.69
103 111 2.357034 GACGCAACGAGGCCTCAA 60.357 61.111 31.67 0.00 0.00 3.02
107 115 2.434185 TCATGACGCAACGAGGCC 60.434 61.111 0.00 0.00 0.00 5.19
113 121 1.416813 CGAGAGCCTCATGACGCAAC 61.417 60.000 17.33 11.17 0.00 4.17
121 129 1.195115 TTGTTAGCCGAGAGCCTCAT 58.805 50.000 0.00 0.00 45.47 2.90
132 140 1.130561 GACTCGCACCATTTGTTAGCC 59.869 52.381 0.00 0.00 0.00 3.93
136 144 1.202758 TCTGGACTCGCACCATTTGTT 60.203 47.619 0.00 0.00 36.79 2.83
141 149 0.687354 AAGTTCTGGACTCGCACCAT 59.313 50.000 0.00 0.00 37.72 3.55
165 186 1.452145 CTCTCGAGGGCCAGCTACTC 61.452 65.000 13.56 0.00 0.00 2.59
168 189 2.123683 CCTCTCGAGGGCCAGCTA 60.124 66.667 13.56 0.00 44.87 3.32
181 202 1.002857 AAAGTATTGCCAGCCCCTCT 58.997 50.000 0.00 0.00 0.00 3.69
203 224 1.430632 GACGATCCTGTTACCGCGA 59.569 57.895 8.23 0.00 0.00 5.87
222 243 1.305381 AAGACGAGGAGGTCCCAGG 60.305 63.158 0.00 0.00 37.66 4.45
224 245 2.283529 GCAAGACGAGGAGGTCCCA 61.284 63.158 0.00 0.00 37.66 4.37
252 274 0.321122 CTGGAACTTGAAGCCGAGCT 60.321 55.000 0.00 0.00 42.56 4.09
266 288 0.400213 CTGGTGTTGTAGGCCTGGAA 59.600 55.000 17.99 4.63 0.00 3.53
273 295 1.016130 CGAGCTGCTGGTGTTGTAGG 61.016 60.000 7.01 0.00 0.00 3.18
276 298 0.671781 GATCGAGCTGCTGGTGTTGT 60.672 55.000 7.01 0.00 0.00 3.32
286 308 1.275953 CTTGCGCATGATCGAGCTG 59.724 57.895 17.78 0.00 32.32 4.24
311 333 2.103042 GGTAGCAGTGCTTCTGGCG 61.103 63.158 25.23 0.00 45.43 5.69
325 347 1.275291 CGCCCTGGTATGGTATGGTAG 59.725 57.143 0.00 0.00 0.00 3.18
330 352 1.623811 GATGTCGCCCTGGTATGGTAT 59.376 52.381 0.00 0.00 0.00 2.73
399 428 5.016173 TGGACCCAGATAAAGTTCAAATGG 58.984 41.667 0.00 0.00 0.00 3.16
401 430 6.015434 GTGTTGGACCCAGATAAAGTTCAAAT 60.015 38.462 0.00 0.00 30.97 2.32
458 686 4.284178 AGGGCATAAATTCAAGACAGCAT 58.716 39.130 0.00 0.00 0.00 3.79
471 699 4.263727 ACAGACACCACATAAGGGCATAAA 60.264 41.667 0.00 0.00 0.00 1.40
478 706 3.738982 TCACAACAGACACCACATAAGG 58.261 45.455 0.00 0.00 0.00 2.69
479 707 4.816385 ACTTCACAACAGACACCACATAAG 59.184 41.667 0.00 0.00 0.00 1.73
483 711 2.290008 ACACTTCACAACAGACACCACA 60.290 45.455 0.00 0.00 0.00 4.17
487 718 4.154195 AGAACAACACTTCACAACAGACAC 59.846 41.667 0.00 0.00 0.00 3.67
493 724 6.687105 GTCACATAAGAACAACACTTCACAAC 59.313 38.462 0.00 0.00 0.00 3.32
502 733 3.814842 CAGCAGGTCACATAAGAACAACA 59.185 43.478 0.00 0.00 0.00 3.33
551 788 7.496263 GTGTTATTTTGCTCACCCCTTTAAAAA 59.504 33.333 0.00 0.00 0.00 1.94
555 792 4.216687 CGTGTTATTTTGCTCACCCCTTTA 59.783 41.667 0.00 0.00 0.00 1.85
574 833 5.393124 CACAGATGTTATTTGATTGCGTGT 58.607 37.500 0.00 0.00 0.00 4.49
582 841 4.277174 ACGCAAACCACAGATGTTATTTGA 59.723 37.500 17.06 0.00 34.58 2.69
587 846 2.805671 CAGACGCAAACCACAGATGTTA 59.194 45.455 0.00 0.00 0.00 2.41
592 851 0.463654 AAGCAGACGCAAACCACAGA 60.464 50.000 0.00 0.00 42.27 3.41
599 858 1.075542 CGGTGATAAGCAGACGCAAA 58.924 50.000 0.00 0.00 42.27 3.68
611 870 4.430007 GTTCTCTGCATTGTACGGTGATA 58.570 43.478 0.00 0.00 0.00 2.15
613 872 2.611971 GGTTCTCTGCATTGTACGGTGA 60.612 50.000 0.00 0.00 0.00 4.02
615 874 1.346395 TGGTTCTCTGCATTGTACGGT 59.654 47.619 0.00 0.00 0.00 4.83
617 876 3.249799 TGTTTGGTTCTCTGCATTGTACG 59.750 43.478 0.00 0.00 0.00 3.67
630 982 7.099266 TCATCATCCATATGTTGTTTGGTTC 57.901 36.000 1.24 0.00 35.29 3.62
686 1039 4.767928 ACACTAGTTGTCCTCCTAGTTGAG 59.232 45.833 0.00 0.00 41.41 3.02
691 1044 4.208746 CCCTACACTAGTTGTCCTCCTAG 58.791 52.174 0.00 0.00 39.91 3.02
693 1046 2.888911 GCCCTACACTAGTTGTCCTCCT 60.889 54.545 0.00 0.00 39.91 3.69
694 1047 1.481363 GCCCTACACTAGTTGTCCTCC 59.519 57.143 0.00 0.00 39.91 4.30
695 1048 1.481363 GGCCCTACACTAGTTGTCCTC 59.519 57.143 0.00 0.00 39.91 3.71
697 1050 1.066358 GTGGCCCTACACTAGTTGTCC 60.066 57.143 0.00 0.00 39.91 4.02
698 1051 1.621814 TGTGGCCCTACACTAGTTGTC 59.378 52.381 0.00 0.00 41.84 3.18
700 1053 3.009723 CAATGTGGCCCTACACTAGTTG 58.990 50.000 0.00 0.00 41.84 3.16
701 1054 2.910319 TCAATGTGGCCCTACACTAGTT 59.090 45.455 0.00 0.00 41.84 2.24
703 1056 3.733337 GATCAATGTGGCCCTACACTAG 58.267 50.000 0.00 0.00 41.84 2.57
704 1057 2.102420 CGATCAATGTGGCCCTACACTA 59.898 50.000 0.00 0.00 41.84 2.74
705 1058 1.134401 CGATCAATGTGGCCCTACACT 60.134 52.381 0.00 0.00 41.84 3.55
706 1059 1.134521 TCGATCAATGTGGCCCTACAC 60.135 52.381 0.00 0.00 41.68 2.90
707 1060 1.138859 CTCGATCAATGTGGCCCTACA 59.861 52.381 0.00 0.00 34.63 2.74
708 1061 1.541233 CCTCGATCAATGTGGCCCTAC 60.541 57.143 0.00 0.00 0.00 3.18
709 1062 0.758734 CCTCGATCAATGTGGCCCTA 59.241 55.000 0.00 0.00 0.00 3.53
710 1063 1.528824 CCTCGATCAATGTGGCCCT 59.471 57.895 0.00 0.00 0.00 5.19
711 1064 1.526917 CCCTCGATCAATGTGGCCC 60.527 63.158 0.00 0.00 0.00 5.80
712 1065 0.533755 CTCCCTCGATCAATGTGGCC 60.534 60.000 0.00 0.00 0.00 5.36
713 1066 0.533755 CCTCCCTCGATCAATGTGGC 60.534 60.000 0.00 0.00 0.00 5.01
714 1067 0.107456 CCCTCCCTCGATCAATGTGG 59.893 60.000 0.00 0.00 0.00 4.17
715 1068 0.833287 ACCCTCCCTCGATCAATGTG 59.167 55.000 0.00 0.00 0.00 3.21
716 1069 0.833287 CACCCTCCCTCGATCAATGT 59.167 55.000 0.00 0.00 0.00 2.71
717 1070 0.833287 ACACCCTCCCTCGATCAATG 59.167 55.000 0.00 0.00 0.00 2.82
718 1071 1.210478 CAACACCCTCCCTCGATCAAT 59.790 52.381 0.00 0.00 0.00 2.57
719 1072 0.613260 CAACACCCTCCCTCGATCAA 59.387 55.000 0.00 0.00 0.00 2.57
720 1073 1.899437 GCAACACCCTCCCTCGATCA 61.899 60.000 0.00 0.00 0.00 2.92
721 1074 1.153349 GCAACACCCTCCCTCGATC 60.153 63.158 0.00 0.00 0.00 3.69
722 1075 2.990479 GCAACACCCTCCCTCGAT 59.010 61.111 0.00 0.00 0.00 3.59
723 1076 3.691342 CGCAACACCCTCCCTCGA 61.691 66.667 0.00 0.00 0.00 4.04
724 1077 4.760047 CCGCAACACCCTCCCTCG 62.760 72.222 0.00 0.00 0.00 4.63
725 1078 2.406002 TTTCCGCAACACCCTCCCTC 62.406 60.000 0.00 0.00 0.00 4.30
726 1079 2.411765 CTTTCCGCAACACCCTCCCT 62.412 60.000 0.00 0.00 0.00 4.20
727 1080 1.971695 CTTTCCGCAACACCCTCCC 60.972 63.158 0.00 0.00 0.00 4.30
728 1081 1.971695 CCTTTCCGCAACACCCTCC 60.972 63.158 0.00 0.00 0.00 4.30
729 1082 0.955919 CTCCTTTCCGCAACACCCTC 60.956 60.000 0.00 0.00 0.00 4.30
730 1083 1.073199 CTCCTTTCCGCAACACCCT 59.927 57.895 0.00 0.00 0.00 4.34
731 1084 0.035739 TACTCCTTTCCGCAACACCC 59.964 55.000 0.00 0.00 0.00 4.61
732 1085 1.886886 TTACTCCTTTCCGCAACACC 58.113 50.000 0.00 0.00 0.00 4.16
739 1092 6.966021 TCAATGTTTTCTTTACTCCTTTCCG 58.034 36.000 0.00 0.00 0.00 4.30
798 1167 1.827399 TTTCGTGCCCCTCCTCAGTC 61.827 60.000 0.00 0.00 0.00 3.51
800 1169 0.674895 CTTTTCGTGCCCCTCCTCAG 60.675 60.000 0.00 0.00 0.00 3.35
801 1170 1.125093 TCTTTTCGTGCCCCTCCTCA 61.125 55.000 0.00 0.00 0.00 3.86
802 1171 0.391793 CTCTTTTCGTGCCCCTCCTC 60.392 60.000 0.00 0.00 0.00 3.71
803 1172 1.128188 ACTCTTTTCGTGCCCCTCCT 61.128 55.000 0.00 0.00 0.00 3.69
809 1178 0.657368 CGTGCAACTCTTTTCGTGCC 60.657 55.000 0.00 0.00 31.75 5.01
815 1184 2.143925 GCTCCTACGTGCAACTCTTTT 58.856 47.619 0.00 0.00 31.75 2.27
831 1200 0.680280 TGTGAGTACCTCCTCGCTCC 60.680 60.000 0.00 0.00 41.50 4.70
835 1204 0.168348 CACGTGTGAGTACCTCCTCG 59.832 60.000 7.58 0.00 34.04 4.63
837 1206 0.111832 TCCACGTGTGAGTACCTCCT 59.888 55.000 15.65 0.00 0.00 3.69
838 1207 0.526662 CTCCACGTGTGAGTACCTCC 59.473 60.000 15.65 0.00 0.00 4.30
839 1208 1.068472 CACTCCACGTGTGAGTACCTC 60.068 57.143 27.93 0.00 38.84 3.85
840 1209 0.959553 CACTCCACGTGTGAGTACCT 59.040 55.000 27.93 11.93 38.84 3.08
841 1210 0.038526 CCACTCCACGTGTGAGTACC 60.039 60.000 27.93 0.00 42.20 3.34
842 1211 0.956633 TCCACTCCACGTGTGAGTAC 59.043 55.000 27.93 0.00 42.20 2.73
843 1212 1.244816 CTCCACTCCACGTGTGAGTA 58.755 55.000 27.93 18.10 42.20 2.59
844 1213 1.464376 CCTCCACTCCACGTGTGAGT 61.464 60.000 24.94 24.94 42.20 3.41
845 1214 1.290324 CCTCCACTCCACGTGTGAG 59.710 63.158 23.93 23.93 42.20 3.51
846 1215 2.867855 GCCTCCACTCCACGTGTGA 61.868 63.158 15.65 10.44 42.20 3.58
847 1216 2.357517 GCCTCCACTCCACGTGTG 60.358 66.667 15.65 9.46 42.20 3.82
848 1217 2.842462 TGCCTCCACTCCACGTGT 60.842 61.111 15.65 0.00 42.20 4.49
849 1218 2.357517 GTGCCTCCACTCCACGTG 60.358 66.667 9.08 9.08 43.41 4.49
866 1235 3.775654 GGGGAGCGGACAGTGGAG 61.776 72.222 0.00 0.00 0.00 3.86
867 1236 4.631740 TGGGGAGCGGACAGTGGA 62.632 66.667 0.00 0.00 0.00 4.02
869 1238 2.788191 GAAGTGGGGAGCGGACAGTG 62.788 65.000 0.00 0.00 0.00 3.66
870 1239 2.526873 AAGTGGGGAGCGGACAGT 60.527 61.111 0.00 0.00 0.00 3.55
871 1240 2.266055 GAAGTGGGGAGCGGACAG 59.734 66.667 0.00 0.00 0.00 3.51
872 1241 3.319198 GGAAGTGGGGAGCGGACA 61.319 66.667 0.00 0.00 0.00 4.02
873 1242 4.097361 GGGAAGTGGGGAGCGGAC 62.097 72.222 0.00 0.00 0.00 4.79
877 1246 3.412408 GGAGGGGAAGTGGGGAGC 61.412 72.222 0.00 0.00 0.00 4.70
896 1279 2.202810 GGAGCGGCGGAGAAGAAG 60.203 66.667 9.78 0.00 0.00 2.85
910 1293 2.823829 GCGGTTAATGCTGGCGGAG 61.824 63.158 0.00 0.00 0.00 4.63
911 1294 2.822255 GCGGTTAATGCTGGCGGA 60.822 61.111 0.00 0.00 0.00 5.54
912 1295 3.130819 TGCGGTTAATGCTGGCGG 61.131 61.111 4.57 0.00 0.00 6.13
913 1296 2.100216 GTGCGGTTAATGCTGGCG 59.900 61.111 4.57 0.00 0.00 5.69
929 1312 4.410033 CCGGGGTAGGAGTGGGGT 62.410 72.222 0.00 0.00 0.00 4.95
988 1382 4.899239 CTCCATGAGGACGCCGGC 62.899 72.222 19.07 19.07 39.61 6.13
1067 1485 3.535629 TTGTCCTCCACGCTGCAGG 62.536 63.158 17.12 8.27 0.00 4.85
1068 1486 2.031012 TTGTCCTCCACGCTGCAG 59.969 61.111 10.11 10.11 0.00 4.41
1069 1487 2.031012 CTTGTCCTCCACGCTGCA 59.969 61.111 0.00 0.00 0.00 4.41
1070 1488 2.743928 CCTTGTCCTCCACGCTGC 60.744 66.667 0.00 0.00 0.00 5.25
1071 1489 2.046892 CCCTTGTCCTCCACGCTG 60.047 66.667 0.00 0.00 0.00 5.18
1072 1490 3.322466 CCCCTTGTCCTCCACGCT 61.322 66.667 0.00 0.00 0.00 5.07
1073 1491 4.410400 CCCCCTTGTCCTCCACGC 62.410 72.222 0.00 0.00 0.00 5.34
1134 1555 0.255890 CGTTGAGGATGGTGGGGATT 59.744 55.000 0.00 0.00 0.00 3.01
1136 1557 2.966732 GCGTTGAGGATGGTGGGGA 61.967 63.158 0.00 0.00 0.00 4.81
1169 1590 3.598562 CGATGCAGTCGTCGTCGC 61.599 66.667 9.48 0.00 45.19 5.19
1206 1627 2.751837 GCCCCCTTTCTTGGAGCG 60.752 66.667 0.00 0.00 0.00 5.03
1207 1628 2.751837 CGCCCCCTTTCTTGGAGC 60.752 66.667 0.00 0.00 0.00 4.70
1302 1738 2.821366 GGCTCGTCGTCGTAGGGA 60.821 66.667 1.33 0.00 38.33 4.20
1423 1862 2.747686 CGTGGTAACCAGGGCAGT 59.252 61.111 0.00 0.00 35.96 4.40
1434 1876 2.889617 CGATGCTGACCCGTGGTA 59.110 61.111 0.00 0.00 35.25 3.25
1436 1878 4.457496 AGCGATGCTGACCCGTGG 62.457 66.667 0.00 0.00 37.57 4.94
1440 1885 1.069204 TCATTAGAGCGATGCTGACCC 59.931 52.381 0.00 0.00 39.88 4.46
1562 2019 3.876198 GGTGGGCTTGCGCATACG 61.876 66.667 12.75 3.93 44.07 3.06
1563 2020 2.749839 TGGTGGGCTTGCGCATAC 60.750 61.111 12.75 6.22 38.10 2.39
1564 2021 2.749839 GTGGTGGGCTTGCGCATA 60.750 61.111 12.75 0.83 38.10 3.14
1569 2026 2.209315 AATGTGGTGGTGGGCTTGC 61.209 57.895 0.00 0.00 0.00 4.01
1585 2042 2.905415 TTTGATGGTCCAGCTCCAAT 57.095 45.000 8.91 0.00 38.52 3.16
1629 2089 2.045536 CTCTTGCTGGGTCCAGGC 60.046 66.667 17.67 10.79 43.77 4.85
1630 2090 1.908340 CTCCTCTTGCTGGGTCCAGG 61.908 65.000 17.67 2.16 43.77 4.45
1653 2113 4.452455 AGTGCGAATGTTACCTTCTTCTTG 59.548 41.667 0.00 0.00 0.00 3.02
1665 2128 3.987404 GCTCCCAGTGCGAATGTT 58.013 55.556 0.00 0.00 0.00 2.71
1713 2179 2.746277 GTAGCAGCACCGGGTTGG 60.746 66.667 6.32 0.00 46.41 3.77
1718 2184 3.958147 CTGTGGGTAGCAGCACCGG 62.958 68.421 0.00 0.00 39.69 5.28
1728 2194 0.179076 CGATGATGCTGCTGTGGGTA 60.179 55.000 0.00 0.00 0.00 3.69
1770 2236 1.172180 TCTTGTTCTTGGCCGGCTTG 61.172 55.000 28.56 16.47 0.00 4.01
1992 2458 4.312941 TGCACGCAGCTGTAGGCA 62.313 61.111 16.64 18.40 45.94 4.75
2290 2756 2.030371 TCTCCATGTAGCTGAGCTGAG 58.970 52.381 18.79 14.39 40.10 3.35
2291 2757 2.149973 TCTCCATGTAGCTGAGCTGA 57.850 50.000 18.79 4.09 40.10 4.26
2292 2758 4.558178 CTTATCTCCATGTAGCTGAGCTG 58.442 47.826 18.79 0.02 40.10 4.24
2293 2759 3.006752 GCTTATCTCCATGTAGCTGAGCT 59.993 47.826 13.25 13.25 43.41 4.09
2294 2760 3.006752 AGCTTATCTCCATGTAGCTGAGC 59.993 47.826 0.00 0.00 40.45 4.26
2295 2761 4.523943 AGAGCTTATCTCCATGTAGCTGAG 59.476 45.833 0.00 0.00 41.90 3.35
2339 2812 3.177228 AGCACCTGGATCACTAACTCTT 58.823 45.455 0.00 0.00 0.00 2.85
2340 2813 2.763448 GAGCACCTGGATCACTAACTCT 59.237 50.000 0.00 0.00 0.00 3.24
2341 2814 2.763448 AGAGCACCTGGATCACTAACTC 59.237 50.000 0.00 0.00 33.23 3.01
2503 2988 4.647564 ACAAGAAGACCAACTGGATCAT 57.352 40.909 1.86 0.00 38.94 2.45
2636 3131 0.730840 TTAGAAGCTCGATCGTCGCA 59.269 50.000 25.44 9.33 40.21 5.10
2713 3208 0.925720 ATCATGCCAAGGGGAGGGAA 60.926 55.000 0.00 0.00 35.59 3.97
3089 3598 5.139435 GATGTTGGTATCCATCATCGAGA 57.861 43.478 18.02 0.00 45.03 4.04
3153 3666 7.702348 GCTGTACACTGAAAAACAAGAAAAGAT 59.298 33.333 0.00 0.00 0.00 2.40
3234 3751 9.343539 GGCTAGTGATGGAATAAAAGAATAAGT 57.656 33.333 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.