Multiple sequence alignment - TraesCS3A01G174200

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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 TraesCS3A01G174200 chr3A 100.000 2641 0 0 1 2641 192848290 192850930 0.000000e+00 4878.0
1 TraesCS3A01G174200 chr1B 92.558 1626 98 14 1021 2641 6352550 6350943 0.000000e+00 2311.0
2 TraesCS3A01G174200 chr1B 97.931 145 3 0 742 886 99709298 99709154 4.360000e-63 252.0
3 TraesCS3A01G174200 chr3B 95.345 1246 47 5 910 2153 559208538 559207302 0.000000e+00 1969.0
4 TraesCS3A01G174200 chr3B 98.582 141 2 0 742 882 242878880 242878740 1.570000e-62 250.0
5 TraesCS3A01G174200 chr3B 97.931 145 2 1 742 885 458386893 458386749 1.570000e-62 250.0
6 TraesCS3A01G174200 chr3B 91.228 57 5 0 2321 2377 787808053 787807997 7.840000e-11 78.7
7 TraesCS3A01G174200 chrUn 95.044 1251 44 9 910 2153 278721756 278722995 0.000000e+00 1951.0
8 TraesCS3A01G174200 chr4B 95.044 1251 44 9 910 2153 28302128 28303367 0.000000e+00 1951.0
9 TraesCS3A01G174200 chr1A 94.744 742 33 2 1 742 410783857 410783122 0.000000e+00 1149.0
10 TraesCS3A01G174200 chr1A 98.630 146 2 0 740 885 514129378 514129523 2.610000e-65 259.0
11 TraesCS3A01G174200 chr6D 93.758 769 35 6 910 1675 133296263 133295505 0.000000e+00 1142.0
12 TraesCS3A01G174200 chr6D 95.000 680 31 2 1962 2641 133295503 133294827 0.000000e+00 1064.0
13 TraesCS3A01G174200 chr4A 79.231 520 79 12 1965 2481 598626760 598627253 4.210000e-88 335.0
14 TraesCS3A01G174200 chr4A 84.674 261 35 4 484 742 541323386 541323129 3.370000e-64 255.0
15 TraesCS3A01G174200 chr4D 85.266 319 38 5 432 742 503801654 503801971 1.180000e-83 320.0
16 TraesCS3A01G174200 chr4D 85.950 242 28 5 504 743 107498422 107498659 1.210000e-63 254.0
17 TraesCS3A01G174200 chr4D 76.883 385 49 13 1 374 503800939 503801294 5.810000e-42 182.0
18 TraesCS3A01G174200 chr2A 86.192 239 32 1 504 742 583826382 583826145 9.380000e-65 257.0
19 TraesCS3A01G174200 chr2B 97.931 145 3 0 742 886 629099622 629099478 4.360000e-63 252.0
20 TraesCS3A01G174200 chr1D 85.833 240 30 4 504 742 481790396 481790160 4.360000e-63 252.0
21 TraesCS3A01G174200 chr1D 81.897 232 39 2 1641 1872 124071289 124071517 2.680000e-45 193.0
22 TraesCS3A01G174200 chr7B 97.917 144 3 0 742 885 418047638 418047495 1.570000e-62 250.0
23 TraesCS3A01G174200 chr7B 79.545 132 22 3 1728 1857 74361416 74361288 3.620000e-14 89.8
24 TraesCS3A01G174200 chr6A 98.582 141 2 0 742 882 603645792 603645932 1.570000e-62 250.0
25 TraesCS3A01G174200 chr2D 84.170 259 36 5 484 741 309583420 309583674 2.030000e-61 246.0
26 TraesCS3A01G174200 chr7A 84.836 244 30 6 503 743 705470360 705470599 3.400000e-59 239.0
27 TraesCS3A01G174200 chr7A 96.992 133 4 0 750 882 679827820 679827952 9.510000e-55 224.0
28 TraesCS3A01G174200 chr7D 95.172 145 7 0 742 886 353937735 353937879 2.040000e-56 230.0
29 TraesCS3A01G174200 chr5D 88.961 154 14 3 568 719 365086871 365086719 1.250000e-43 187.0
30 TraesCS3A01G174200 chr5D 85.000 160 19 5 1696 1854 420604184 420604339 9.790000e-35 158.0
31 TraesCS3A01G174200 chr5D 79.429 175 30 6 1686 1858 483980680 483980510 4.620000e-23 119.0
32 TraesCS3A01G174200 chr5D 83.607 122 18 2 1737 1858 483984355 483984236 2.150000e-21 113.0


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 TraesCS3A01G174200 chr3A 192848290 192850930 2640 False 4878 4878 100.0000 1 2641 1 chr3A.!!$F1 2640
1 TraesCS3A01G174200 chr1B 6350943 6352550 1607 True 2311 2311 92.5580 1021 2641 1 chr1B.!!$R1 1620
2 TraesCS3A01G174200 chr3B 559207302 559208538 1236 True 1969 1969 95.3450 910 2153 1 chr3B.!!$R3 1243
3 TraesCS3A01G174200 chrUn 278721756 278722995 1239 False 1951 1951 95.0440 910 2153 1 chrUn.!!$F1 1243
4 TraesCS3A01G174200 chr4B 28302128 28303367 1239 False 1951 1951 95.0440 910 2153 1 chr4B.!!$F1 1243
5 TraesCS3A01G174200 chr1A 410783122 410783857 735 True 1149 1149 94.7440 1 742 1 chr1A.!!$R1 741
6 TraesCS3A01G174200 chr6D 133294827 133296263 1436 True 1103 1142 94.3790 910 2641 2 chr6D.!!$R1 1731
7 TraesCS3A01G174200 chr4D 503800939 503801971 1032 False 251 320 81.0745 1 742 2 chr4D.!!$F2 741

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
888 1216 0.036306 CCGAACAGGGCTTAAGTGGT 59.964 55.0 4.02 0.0 35.97 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 2211 0.104487 CTGCCATTGCCACACAACAA 59.896 50.0 0.0 0.0 42.27 2.83 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
109 110 0.249398 GCTTGTGTAGGTCGTCCCAT 59.751 55.000 0.00 0.00 34.66 4.00
193 194 4.221422 GCATGACCGCCGCCTCTA 62.221 66.667 0.00 0.00 0.00 2.43
194 195 2.737180 CATGACCGCCGCCTCTAT 59.263 61.111 0.00 0.00 0.00 1.98
195 196 1.665916 CATGACCGCCGCCTCTATG 60.666 63.158 0.00 0.00 0.00 2.23
196 197 3.521529 ATGACCGCCGCCTCTATGC 62.522 63.158 0.00 0.00 0.00 3.14
197 198 4.221422 GACCGCCGCCTCTATGCA 62.221 66.667 0.00 0.00 0.00 3.96
198 199 4.227134 ACCGCCGCCTCTATGCAG 62.227 66.667 0.00 0.00 0.00 4.41
201 202 2.280457 GCCGCCTCTATGCAGGTC 60.280 66.667 0.00 0.00 35.72 3.85
267 285 2.397597 TGTCTAGCTGCACCATGGATA 58.602 47.619 21.47 2.79 0.00 2.59
693 1021 3.066760 AGTGCAAAGTAAAGAGTGGCAAC 59.933 43.478 0.00 0.00 0.00 4.17
742 1070 7.712639 TGGCAAATTATCAAAGTGCAAAGTAAA 59.287 29.630 0.00 0.00 0.00 2.01
743 1071 8.223100 GGCAAATTATCAAAGTGCAAAGTAAAG 58.777 33.333 0.00 0.00 0.00 1.85
744 1072 8.223100 GCAAATTATCAAAGTGCAAAGTAAAGG 58.777 33.333 0.00 0.00 0.00 3.11
745 1073 7.889589 AATTATCAAAGTGCAAAGTAAAGGC 57.110 32.000 0.00 0.00 0.00 4.35
746 1074 3.726291 TCAAAGTGCAAAGTAAAGGCC 57.274 42.857 0.00 0.00 0.00 5.19
747 1075 3.295973 TCAAAGTGCAAAGTAAAGGCCT 58.704 40.909 0.00 0.00 0.00 5.19
748 1076 3.068024 TCAAAGTGCAAAGTAAAGGCCTG 59.932 43.478 5.69 0.00 0.00 4.85
749 1077 2.364972 AGTGCAAAGTAAAGGCCTGT 57.635 45.000 5.69 1.77 0.00 4.00
750 1078 2.666317 AGTGCAAAGTAAAGGCCTGTT 58.334 42.857 5.69 5.66 0.00 3.16
751 1079 2.623416 AGTGCAAAGTAAAGGCCTGTTC 59.377 45.455 5.69 0.00 0.00 3.18
752 1080 1.606668 TGCAAAGTAAAGGCCTGTTCG 59.393 47.619 5.69 0.00 0.00 3.95
753 1081 1.068541 GCAAAGTAAAGGCCTGTTCGG 60.069 52.381 5.69 0.00 0.00 4.30
754 1082 2.227194 CAAAGTAAAGGCCTGTTCGGT 58.773 47.619 5.69 0.00 34.25 4.69
755 1083 3.404899 CAAAGTAAAGGCCTGTTCGGTA 58.595 45.455 5.69 0.00 34.25 4.02
756 1084 3.994931 AAGTAAAGGCCTGTTCGGTAT 57.005 42.857 5.69 0.00 34.25 2.73
757 1085 3.538634 AGTAAAGGCCTGTTCGGTATC 57.461 47.619 5.69 0.00 34.25 2.24
758 1086 3.105283 AGTAAAGGCCTGTTCGGTATCT 58.895 45.455 5.69 0.00 34.25 1.98
759 1087 2.693267 AAAGGCCTGTTCGGTATCTC 57.307 50.000 5.69 0.00 34.25 2.75
760 1088 0.460311 AAGGCCTGTTCGGTATCTCG 59.540 55.000 5.69 0.00 34.25 4.04
761 1089 1.591863 GGCCTGTTCGGTATCTCGC 60.592 63.158 0.00 0.00 34.25 5.03
762 1090 1.591863 GCCTGTTCGGTATCTCGCC 60.592 63.158 0.00 0.00 34.25 5.54
763 1091 1.813859 CCTGTTCGGTATCTCGCCA 59.186 57.895 0.00 0.00 0.00 5.69
764 1092 0.174845 CCTGTTCGGTATCTCGCCAA 59.825 55.000 0.00 0.00 0.00 4.52
765 1093 1.202533 CCTGTTCGGTATCTCGCCAAT 60.203 52.381 0.00 0.00 0.00 3.16
766 1094 2.550978 CTGTTCGGTATCTCGCCAATT 58.449 47.619 0.00 0.00 0.00 2.32
767 1095 2.936498 CTGTTCGGTATCTCGCCAATTT 59.064 45.455 0.00 0.00 0.00 1.82
768 1096 2.933906 TGTTCGGTATCTCGCCAATTTC 59.066 45.455 0.00 0.00 0.00 2.17
769 1097 2.933906 GTTCGGTATCTCGCCAATTTCA 59.066 45.455 0.00 0.00 0.00 2.69
770 1098 3.254470 TCGGTATCTCGCCAATTTCAA 57.746 42.857 0.00 0.00 0.00 2.69
771 1099 3.601435 TCGGTATCTCGCCAATTTCAAA 58.399 40.909 0.00 0.00 0.00 2.69
772 1100 4.004314 TCGGTATCTCGCCAATTTCAAAA 58.996 39.130 0.00 0.00 0.00 2.44
773 1101 4.095610 CGGTATCTCGCCAATTTCAAAAC 58.904 43.478 0.00 0.00 0.00 2.43
774 1102 4.142687 CGGTATCTCGCCAATTTCAAAACT 60.143 41.667 0.00 0.00 0.00 2.66
775 1103 5.332707 GGTATCTCGCCAATTTCAAAACTC 58.667 41.667 0.00 0.00 0.00 3.01
776 1104 3.915437 TCTCGCCAATTTCAAAACTCC 57.085 42.857 0.00 0.00 0.00 3.85
777 1105 2.225491 TCTCGCCAATTTCAAAACTCCG 59.775 45.455 0.00 0.00 0.00 4.63
778 1106 1.059942 CGCCAATTTCAAAACTCCGC 58.940 50.000 0.00 0.00 0.00 5.54
779 1107 1.335872 CGCCAATTTCAAAACTCCGCT 60.336 47.619 0.00 0.00 0.00 5.52
780 1108 2.328473 GCCAATTTCAAAACTCCGCTC 58.672 47.619 0.00 0.00 0.00 5.03
781 1109 2.926586 GCCAATTTCAAAACTCCGCTCC 60.927 50.000 0.00 0.00 0.00 4.70
782 1110 2.584791 CAATTTCAAAACTCCGCTCCG 58.415 47.619 0.00 0.00 0.00 4.63
783 1111 1.892209 ATTTCAAAACTCCGCTCCGT 58.108 45.000 0.00 0.00 0.00 4.69
784 1112 0.941542 TTTCAAAACTCCGCTCCGTG 59.058 50.000 0.00 0.00 0.00 4.94
785 1113 1.503818 TTCAAAACTCCGCTCCGTGC 61.504 55.000 0.00 0.00 38.57 5.34
786 1114 1.961277 CAAAACTCCGCTCCGTGCT 60.961 57.895 0.00 0.00 40.11 4.40
787 1115 0.669318 CAAAACTCCGCTCCGTGCTA 60.669 55.000 0.00 0.00 40.11 3.49
788 1116 0.389948 AAAACTCCGCTCCGTGCTAG 60.390 55.000 0.00 0.00 40.11 3.42
789 1117 2.227089 AAACTCCGCTCCGTGCTAGG 62.227 60.000 0.00 0.00 40.11 3.02
790 1118 2.829003 CTCCGCTCCGTGCTAGGA 60.829 66.667 0.00 1.01 40.11 2.94
796 1124 2.037367 TCCGTGCTAGGAGCTGGT 59.963 61.111 0.00 0.00 42.97 4.00
797 1125 1.609501 TCCGTGCTAGGAGCTGGTT 60.610 57.895 0.00 0.00 42.97 3.67
798 1126 1.153549 CCGTGCTAGGAGCTGGTTC 60.154 63.158 0.00 0.00 42.97 3.62
799 1127 1.153549 CGTGCTAGGAGCTGGTTCC 60.154 63.158 0.00 0.00 42.97 3.62
800 1128 1.153549 GTGCTAGGAGCTGGTTCCG 60.154 63.158 0.00 0.00 42.97 4.30
801 1129 1.304962 TGCTAGGAGCTGGTTCCGA 60.305 57.895 0.00 0.00 42.97 4.55
802 1130 1.323271 TGCTAGGAGCTGGTTCCGAG 61.323 60.000 8.68 8.68 42.97 4.63
803 1131 1.439644 CTAGGAGCTGGTTCCGAGC 59.560 63.158 0.00 0.00 42.29 5.03
804 1132 2.022240 CTAGGAGCTGGTTCCGAGCC 62.022 65.000 0.00 0.00 42.29 4.70
805 1133 2.798445 TAGGAGCTGGTTCCGAGCCA 62.798 60.000 3.68 3.68 42.29 4.75
806 1134 2.435059 GAGCTGGTTCCGAGCCAC 60.435 66.667 0.00 0.00 37.12 5.01
807 1135 2.925170 AGCTGGTTCCGAGCCACT 60.925 61.111 0.00 0.76 37.12 4.00
808 1136 2.435059 GCTGGTTCCGAGCCACTC 60.435 66.667 0.00 0.00 31.85 3.51
809 1137 2.266055 CTGGTTCCGAGCCACTCC 59.734 66.667 0.00 0.00 31.85 3.85
810 1138 3.649277 CTGGTTCCGAGCCACTCCG 62.649 68.421 0.00 0.00 31.85 4.63
811 1139 3.692406 GGTTCCGAGCCACTCCGT 61.692 66.667 0.00 0.00 0.00 4.69
812 1140 2.345760 GGTTCCGAGCCACTCCGTA 61.346 63.158 0.00 0.00 0.00 4.02
813 1141 1.139095 GTTCCGAGCCACTCCGTAG 59.861 63.158 0.00 0.00 0.00 3.51
826 1154 4.420143 CGTAGGATTCCACTGCCG 57.580 61.111 5.29 0.00 0.00 5.69
827 1155 1.883084 CGTAGGATTCCACTGCCGC 60.883 63.158 5.29 0.00 0.00 6.53
828 1156 1.522569 GTAGGATTCCACTGCCGCT 59.477 57.895 5.29 0.00 0.00 5.52
829 1157 0.530870 GTAGGATTCCACTGCCGCTC 60.531 60.000 5.29 0.00 0.00 5.03
830 1158 1.686325 TAGGATTCCACTGCCGCTCC 61.686 60.000 5.29 0.00 0.00 4.70
831 1159 2.514824 GATTCCACTGCCGCTCCC 60.515 66.667 0.00 0.00 0.00 4.30
832 1160 3.011517 ATTCCACTGCCGCTCCCT 61.012 61.111 0.00 0.00 0.00 4.20
833 1161 2.932130 GATTCCACTGCCGCTCCCTC 62.932 65.000 0.00 0.00 0.00 4.30
858 1186 4.803426 GGAGTCGCAGCCGTGGAG 62.803 72.222 0.00 0.00 35.54 3.86
867 1195 4.373116 GCCGTGGAGCCGAGTGAA 62.373 66.667 0.00 0.00 0.00 3.18
868 1196 2.579201 CCGTGGAGCCGAGTGAAT 59.421 61.111 0.00 0.00 0.00 2.57
869 1197 1.519455 CCGTGGAGCCGAGTGAATC 60.519 63.158 0.00 0.00 0.00 2.52
870 1198 1.519455 CGTGGAGCCGAGTGAATCC 60.519 63.158 0.00 0.00 0.00 3.01
871 1199 1.519455 GTGGAGCCGAGTGAATCCG 60.519 63.158 0.00 0.00 34.39 4.18
872 1200 1.680989 TGGAGCCGAGTGAATCCGA 60.681 57.895 0.00 0.00 34.39 4.55
873 1201 1.254975 TGGAGCCGAGTGAATCCGAA 61.255 55.000 0.00 0.00 34.39 4.30
874 1202 0.806492 GGAGCCGAGTGAATCCGAAC 60.806 60.000 0.00 0.00 0.00 3.95
875 1203 0.108804 GAGCCGAGTGAATCCGAACA 60.109 55.000 0.00 0.00 0.00 3.18
876 1204 0.108615 AGCCGAGTGAATCCGAACAG 60.109 55.000 0.00 0.00 0.00 3.16
877 1205 1.084370 GCCGAGTGAATCCGAACAGG 61.084 60.000 0.00 0.00 42.97 4.00
878 1206 0.460284 CCGAGTGAATCCGAACAGGG 60.460 60.000 0.00 0.00 41.52 4.45
879 1207 1.084370 CGAGTGAATCCGAACAGGGC 61.084 60.000 0.00 0.00 41.52 5.19
880 1208 0.250513 GAGTGAATCCGAACAGGGCT 59.749 55.000 0.00 0.00 41.52 5.19
881 1209 0.693049 AGTGAATCCGAACAGGGCTT 59.307 50.000 0.00 0.00 41.52 4.35
882 1210 1.906574 AGTGAATCCGAACAGGGCTTA 59.093 47.619 0.00 0.00 41.52 3.09
883 1211 2.304761 AGTGAATCCGAACAGGGCTTAA 59.695 45.455 0.00 0.00 41.52 1.85
884 1212 2.678336 GTGAATCCGAACAGGGCTTAAG 59.322 50.000 0.00 0.00 41.52 1.85
885 1213 2.304761 TGAATCCGAACAGGGCTTAAGT 59.695 45.455 4.02 0.00 41.52 2.24
886 1214 2.403252 ATCCGAACAGGGCTTAAGTG 57.597 50.000 4.02 0.00 41.52 3.16
887 1215 0.323629 TCCGAACAGGGCTTAAGTGG 59.676 55.000 4.02 0.00 41.52 4.00
888 1216 0.036306 CCGAACAGGGCTTAAGTGGT 59.964 55.000 4.02 0.00 35.97 4.16
889 1217 1.156736 CGAACAGGGCTTAAGTGGTG 58.843 55.000 4.02 1.80 0.00 4.17
890 1218 1.534729 GAACAGGGCTTAAGTGGTGG 58.465 55.000 4.02 0.00 0.00 4.61
891 1219 0.539669 AACAGGGCTTAAGTGGTGGC 60.540 55.000 4.02 0.00 0.00 5.01
892 1220 1.074775 CAGGGCTTAAGTGGTGGCA 59.925 57.895 4.02 0.00 0.00 4.92
893 1221 0.539438 CAGGGCTTAAGTGGTGGCAA 60.539 55.000 4.02 0.00 0.00 4.52
894 1222 0.187361 AGGGCTTAAGTGGTGGCAAA 59.813 50.000 4.02 0.00 0.00 3.68
895 1223 1.044611 GGGCTTAAGTGGTGGCAAAA 58.955 50.000 4.02 0.00 0.00 2.44
896 1224 1.414550 GGGCTTAAGTGGTGGCAAAAA 59.585 47.619 4.02 0.00 0.00 1.94
897 1225 2.547855 GGGCTTAAGTGGTGGCAAAAAG 60.548 50.000 4.02 0.00 0.00 2.27
898 1226 2.102420 GGCTTAAGTGGTGGCAAAAAGT 59.898 45.455 4.02 0.00 0.00 2.66
899 1227 3.381045 GCTTAAGTGGTGGCAAAAAGTC 58.619 45.455 4.02 0.00 0.00 3.01
900 1228 3.181480 GCTTAAGTGGTGGCAAAAAGTCA 60.181 43.478 4.02 0.00 0.00 3.41
901 1229 4.679372 GCTTAAGTGGTGGCAAAAAGTCAA 60.679 41.667 4.02 0.00 30.62 3.18
902 1230 3.971245 AAGTGGTGGCAAAAAGTCAAA 57.029 38.095 0.00 0.00 30.62 2.69
903 1231 3.971245 AGTGGTGGCAAAAAGTCAAAA 57.029 38.095 0.00 0.00 30.62 2.44
904 1232 4.278975 AGTGGTGGCAAAAAGTCAAAAA 57.721 36.364 0.00 0.00 30.62 1.94
905 1233 4.000325 AGTGGTGGCAAAAAGTCAAAAAC 59.000 39.130 0.00 0.00 30.62 2.43
906 1234 3.126171 GTGGTGGCAAAAAGTCAAAAACC 59.874 43.478 0.00 0.00 30.62 3.27
907 1235 2.680841 GGTGGCAAAAAGTCAAAAACCC 59.319 45.455 0.00 0.00 30.62 4.11
908 1236 2.680841 GTGGCAAAAAGTCAAAAACCCC 59.319 45.455 0.00 0.00 30.62 4.95
1138 1467 1.134936 TCTTATTAGTGCGCGCCTTCA 60.135 47.619 30.77 14.87 0.00 3.02
1250 1580 1.860641 TCAGTATCGGTGATGTGGGT 58.139 50.000 0.00 0.00 0.00 4.51
1272 1602 3.039202 GCGGCGGTGACATTGGAAG 62.039 63.158 9.78 0.00 0.00 3.46
1428 1758 7.042456 CCTGTAAATTCGACTGGACTGATAATG 60.042 40.741 9.54 0.00 37.96 1.90
1431 1763 6.910536 AATTCGACTGGACTGATAATGTTC 57.089 37.500 0.00 0.00 0.00 3.18
1768 2102 9.403583 GACTATTACAATTTGTATTCCTGGGAA 57.596 33.333 9.95 4.43 38.59 3.97
1772 2106 9.889128 ATTACAATTTGTATTCCTGGGAAATTG 57.111 29.630 9.95 16.08 44.24 2.32
1773 2107 6.710278 ACAATTTGTATTCCTGGGAAATTGG 58.290 36.000 19.30 8.63 43.52 3.16
1994 2333 0.977108 GGCATTTGCAGGGGATTCCA 60.977 55.000 4.80 0.00 44.36 3.53
1995 2334 1.125633 GCATTTGCAGGGGATTCCAT 58.874 50.000 4.80 0.00 41.59 3.41
2101 2440 4.825422 AGTGAGTTCATACCATCACACAG 58.175 43.478 6.91 0.00 43.55 3.66
2108 2447 3.200605 TCATACCATCACACAGCCATTCT 59.799 43.478 0.00 0.00 0.00 2.40
2127 2466 4.365514 TCTTTAATGGAGAAGTGTGGCA 57.634 40.909 0.00 0.00 0.00 4.92
2194 2533 3.146066 GTGATGTGGTTAAGCAACTCCA 58.854 45.455 9.30 3.51 34.88 3.86
2234 2573 7.927629 AGCATTGGCAAGGTTTACAATATAATG 59.072 33.333 13.90 0.00 44.61 1.90
2236 2575 7.962995 TTGGCAAGGTTTACAATATAATGGA 57.037 32.000 0.00 0.00 0.00 3.41
2273 2612 3.770388 TCAATGTCCAATGTGCCATTCAT 59.230 39.130 0.00 0.00 0.00 2.57
2442 2781 4.776795 ACGGAATTTGTTATGGTCAACC 57.223 40.909 0.00 0.00 0.00 3.77
2481 2820 1.813513 ACCACTTCTTTGGAGATGCG 58.186 50.000 0.00 0.00 39.24 4.73
2516 2855 2.134789 ACATACCGTACCGACCTCTT 57.865 50.000 0.00 0.00 0.00 2.85
2552 2891 1.949525 CCTGTTTGTGGGAGTCAACAG 59.050 52.381 11.51 11.51 0.00 3.16
2553 2892 2.421388 CCTGTTTGTGGGAGTCAACAGA 60.421 50.000 17.49 3.76 31.93 3.41
2560 2899 2.103263 GTGGGAGTCAACAGACACTTCT 59.897 50.000 0.00 0.00 34.69 2.85
2589 2928 2.684001 TATTTGGTGGCGTCCTAGTG 57.316 50.000 0.00 0.00 0.00 2.74
2600 2939 2.289547 GCGTCCTAGTGAGAGATGAGAC 59.710 54.545 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 182 4.227134 CTGCATAGAGGCGGCGGT 62.227 66.667 9.78 0.00 36.28 5.68
193 194 1.884579 CTTGCTGTTGAAGACCTGCAT 59.115 47.619 0.00 0.00 36.87 3.96
194 195 1.311859 CTTGCTGTTGAAGACCTGCA 58.688 50.000 0.00 0.00 35.77 4.41
195 196 0.595095 CCTTGCTGTTGAAGACCTGC 59.405 55.000 0.00 0.00 0.00 4.85
196 197 2.260844 TCCTTGCTGTTGAAGACCTG 57.739 50.000 0.00 0.00 0.00 4.00
197 198 2.576615 GTTCCTTGCTGTTGAAGACCT 58.423 47.619 0.00 0.00 0.00 3.85
198 199 1.264288 CGTTCCTTGCTGTTGAAGACC 59.736 52.381 0.00 0.00 0.00 3.85
201 202 0.040067 GGCGTTCCTTGCTGTTGAAG 60.040 55.000 0.00 0.00 0.00 3.02
267 285 2.616510 GGCTCTGTACATGGTGCTCTTT 60.617 50.000 0.00 0.00 0.00 2.52
379 397 1.671328 TGGTAGAAGAGCTCGATGTCG 59.329 52.381 8.37 0.00 41.45 4.35
693 1021 7.485913 GCCACTCATTACATTGTAATTGACTTG 59.514 37.037 17.42 8.75 0.00 3.16
712 1040 4.280425 TGCACTTTGATAATTTGCCACTCA 59.720 37.500 0.00 0.00 0.00 3.41
742 1070 2.017559 GCGAGATACCGAACAGGCCT 62.018 60.000 0.00 0.00 46.52 5.19
743 1071 1.591863 GCGAGATACCGAACAGGCC 60.592 63.158 0.00 0.00 46.52 5.19
744 1072 1.591863 GGCGAGATACCGAACAGGC 60.592 63.158 0.00 0.00 46.52 4.85
746 1074 2.225068 ATTGGCGAGATACCGAACAG 57.775 50.000 0.00 0.00 0.00 3.16
747 1075 2.684001 AATTGGCGAGATACCGAACA 57.316 45.000 0.00 0.00 0.00 3.18
748 1076 2.933906 TGAAATTGGCGAGATACCGAAC 59.066 45.455 0.00 0.00 0.00 3.95
749 1077 3.254470 TGAAATTGGCGAGATACCGAA 57.746 42.857 0.00 0.00 0.00 4.30
750 1078 2.971660 TGAAATTGGCGAGATACCGA 57.028 45.000 0.00 0.00 0.00 4.69
751 1079 4.095610 GTTTTGAAATTGGCGAGATACCG 58.904 43.478 0.00 0.00 0.00 4.02
752 1080 5.310720 AGTTTTGAAATTGGCGAGATACC 57.689 39.130 0.00 0.00 0.00 2.73
753 1081 5.332707 GGAGTTTTGAAATTGGCGAGATAC 58.667 41.667 0.00 0.00 0.00 2.24
754 1082 4.094294 CGGAGTTTTGAAATTGGCGAGATA 59.906 41.667 0.00 0.00 0.00 1.98
755 1083 3.119849 CGGAGTTTTGAAATTGGCGAGAT 60.120 43.478 0.00 0.00 0.00 2.75
756 1084 2.225491 CGGAGTTTTGAAATTGGCGAGA 59.775 45.455 0.00 0.00 0.00 4.04
757 1085 2.584791 CGGAGTTTTGAAATTGGCGAG 58.415 47.619 0.00 0.00 0.00 5.03
758 1086 1.335506 GCGGAGTTTTGAAATTGGCGA 60.336 47.619 0.00 0.00 0.00 5.54
759 1087 1.059942 GCGGAGTTTTGAAATTGGCG 58.940 50.000 0.00 0.00 0.00 5.69
760 1088 2.328473 GAGCGGAGTTTTGAAATTGGC 58.672 47.619 0.00 0.00 0.00 4.52
761 1089 2.668279 CGGAGCGGAGTTTTGAAATTGG 60.668 50.000 0.00 0.00 0.00 3.16
762 1090 2.031157 ACGGAGCGGAGTTTTGAAATTG 60.031 45.455 0.00 0.00 0.00 2.32
763 1091 2.031157 CACGGAGCGGAGTTTTGAAATT 60.031 45.455 0.00 0.00 0.00 1.82
764 1092 1.535462 CACGGAGCGGAGTTTTGAAAT 59.465 47.619 0.00 0.00 0.00 2.17
765 1093 0.941542 CACGGAGCGGAGTTTTGAAA 59.058 50.000 0.00 0.00 0.00 2.69
766 1094 1.503818 GCACGGAGCGGAGTTTTGAA 61.504 55.000 0.00 0.00 0.00 2.69
767 1095 1.959226 GCACGGAGCGGAGTTTTGA 60.959 57.895 0.00 0.00 0.00 2.69
768 1096 2.556287 GCACGGAGCGGAGTTTTG 59.444 61.111 0.00 0.00 0.00 2.44
779 1107 1.605058 GAACCAGCTCCTAGCACGGA 61.605 60.000 12.67 0.00 45.56 4.69
780 1108 1.153549 GAACCAGCTCCTAGCACGG 60.154 63.158 1.22 3.98 45.56 4.94
781 1109 1.153549 GGAACCAGCTCCTAGCACG 60.154 63.158 1.22 0.00 45.56 5.34
782 1110 1.153549 CGGAACCAGCTCCTAGCAC 60.154 63.158 1.22 0.00 45.56 4.40
783 1111 1.304962 TCGGAACCAGCTCCTAGCA 60.305 57.895 1.22 0.00 45.56 3.49
784 1112 1.439644 CTCGGAACCAGCTCCTAGC 59.560 63.158 0.00 0.00 42.84 3.42
785 1113 1.439644 GCTCGGAACCAGCTCCTAG 59.560 63.158 0.00 0.00 33.75 3.02
786 1114 2.058595 GGCTCGGAACCAGCTCCTA 61.059 63.158 12.30 0.00 37.05 2.94
787 1115 3.394836 GGCTCGGAACCAGCTCCT 61.395 66.667 12.30 0.00 37.05 3.69
788 1116 3.706373 TGGCTCGGAACCAGCTCC 61.706 66.667 0.00 0.00 37.05 4.70
789 1117 2.435059 GTGGCTCGGAACCAGCTC 60.435 66.667 0.00 0.00 38.04 4.09
790 1118 2.925170 AGTGGCTCGGAACCAGCT 60.925 61.111 0.00 0.00 38.04 4.24
791 1119 2.435059 GAGTGGCTCGGAACCAGC 60.435 66.667 0.00 0.00 38.04 4.85
792 1120 2.266055 GGAGTGGCTCGGAACCAG 59.734 66.667 0.00 0.00 38.04 4.00
793 1121 3.691342 CGGAGTGGCTCGGAACCA 61.691 66.667 0.00 0.00 33.52 3.67
794 1122 2.280823 CTACGGAGTGGCTCGGAACC 62.281 65.000 10.03 0.00 45.73 3.62
795 1123 1.139095 CTACGGAGTGGCTCGGAAC 59.861 63.158 10.03 0.00 45.73 3.62
796 1124 2.050350 CCTACGGAGTGGCTCGGAA 61.050 63.158 10.03 0.00 45.73 4.30
797 1125 2.280404 ATCCTACGGAGTGGCTCGGA 62.280 60.000 10.03 2.66 45.73 4.55
798 1126 1.392710 AATCCTACGGAGTGGCTCGG 61.393 60.000 0.00 2.79 45.73 4.63
799 1127 0.030908 GAATCCTACGGAGTGGCTCG 59.969 60.000 0.00 0.00 45.73 5.03
800 1128 0.389757 GGAATCCTACGGAGTGGCTC 59.610 60.000 0.00 0.00 45.73 4.70
801 1129 0.325296 TGGAATCCTACGGAGTGGCT 60.325 55.000 0.00 0.00 45.73 4.75
802 1130 0.179081 GTGGAATCCTACGGAGTGGC 60.179 60.000 0.00 0.00 45.73 5.01
803 1131 1.137086 CAGTGGAATCCTACGGAGTGG 59.863 57.143 0.00 0.00 45.73 4.00
804 1132 1.471676 GCAGTGGAATCCTACGGAGTG 60.472 57.143 0.00 0.00 45.73 3.51
806 1134 0.105039 GGCAGTGGAATCCTACGGAG 59.895 60.000 0.00 0.00 34.05 4.63
807 1135 1.672854 CGGCAGTGGAATCCTACGGA 61.673 60.000 0.00 0.00 35.55 4.69
808 1136 1.227263 CGGCAGTGGAATCCTACGG 60.227 63.158 0.00 0.00 0.00 4.02
809 1137 1.883084 GCGGCAGTGGAATCCTACG 60.883 63.158 0.00 0.00 0.00 3.51
810 1138 0.530870 GAGCGGCAGTGGAATCCTAC 60.531 60.000 1.45 0.00 0.00 3.18
811 1139 1.686325 GGAGCGGCAGTGGAATCCTA 61.686 60.000 1.45 0.00 0.00 2.94
812 1140 2.586792 GAGCGGCAGTGGAATCCT 59.413 61.111 1.45 0.00 0.00 3.24
813 1141 2.514824 GGAGCGGCAGTGGAATCC 60.515 66.667 1.45 0.00 0.00 3.01
814 1142 2.514824 GGGAGCGGCAGTGGAATC 60.515 66.667 1.45 0.00 0.00 2.52
815 1143 3.011517 AGGGAGCGGCAGTGGAAT 61.012 61.111 1.45 0.00 0.00 3.01
816 1144 3.706373 GAGGGAGCGGCAGTGGAA 61.706 66.667 1.45 0.00 0.00 3.53
841 1169 4.803426 CTCCACGGCTGCGACTCC 62.803 72.222 0.00 0.00 0.00 3.85
850 1178 3.665675 ATTCACTCGGCTCCACGGC 62.666 63.158 0.00 0.00 0.00 5.68
851 1179 1.519455 GATTCACTCGGCTCCACGG 60.519 63.158 0.00 0.00 0.00 4.94
852 1180 1.519455 GGATTCACTCGGCTCCACG 60.519 63.158 0.00 0.00 0.00 4.94
853 1181 1.519455 CGGATTCACTCGGCTCCAC 60.519 63.158 0.00 0.00 0.00 4.02
854 1182 1.254975 TTCGGATTCACTCGGCTCCA 61.255 55.000 0.00 0.00 0.00 3.86
855 1183 0.806492 GTTCGGATTCACTCGGCTCC 60.806 60.000 0.00 0.00 0.00 4.70
856 1184 0.108804 TGTTCGGATTCACTCGGCTC 60.109 55.000 0.00 0.00 0.00 4.70
857 1185 0.108615 CTGTTCGGATTCACTCGGCT 60.109 55.000 0.00 0.00 0.00 5.52
858 1186 1.084370 CCTGTTCGGATTCACTCGGC 61.084 60.000 0.00 0.00 33.16 5.54
859 1187 0.460284 CCCTGTTCGGATTCACTCGG 60.460 60.000 0.00 0.00 33.16 4.63
860 1188 1.084370 GCCCTGTTCGGATTCACTCG 61.084 60.000 0.00 0.00 33.16 4.18
861 1189 0.250513 AGCCCTGTTCGGATTCACTC 59.749 55.000 0.00 0.00 33.16 3.51
862 1190 0.693049 AAGCCCTGTTCGGATTCACT 59.307 50.000 0.00 0.00 33.16 3.41
863 1191 2.396590 TAAGCCCTGTTCGGATTCAC 57.603 50.000 0.00 0.00 32.63 3.18
864 1192 2.304761 ACTTAAGCCCTGTTCGGATTCA 59.695 45.455 1.29 0.00 32.63 2.57
865 1193 2.678336 CACTTAAGCCCTGTTCGGATTC 59.322 50.000 1.29 0.00 32.63 2.52
866 1194 2.618045 CCACTTAAGCCCTGTTCGGATT 60.618 50.000 1.29 0.00 35.25 3.01
867 1195 1.065418 CCACTTAAGCCCTGTTCGGAT 60.065 52.381 1.29 0.00 33.16 4.18
868 1196 0.323629 CCACTTAAGCCCTGTTCGGA 59.676 55.000 1.29 0.00 33.16 4.55
869 1197 0.036306 ACCACTTAAGCCCTGTTCGG 59.964 55.000 1.29 0.00 0.00 4.30
870 1198 1.156736 CACCACTTAAGCCCTGTTCG 58.843 55.000 1.29 0.00 0.00 3.95
871 1199 1.534729 CCACCACTTAAGCCCTGTTC 58.465 55.000 1.29 0.00 0.00 3.18
872 1200 0.539669 GCCACCACTTAAGCCCTGTT 60.540 55.000 1.29 0.00 0.00 3.16
873 1201 1.074951 GCCACCACTTAAGCCCTGT 59.925 57.895 1.29 0.00 0.00 4.00
874 1202 0.539438 TTGCCACCACTTAAGCCCTG 60.539 55.000 1.29 0.00 0.00 4.45
875 1203 0.187361 TTTGCCACCACTTAAGCCCT 59.813 50.000 1.29 0.00 0.00 5.19
876 1204 1.044611 TTTTGCCACCACTTAAGCCC 58.955 50.000 1.29 0.00 0.00 5.19
877 1205 2.102420 ACTTTTTGCCACCACTTAAGCC 59.898 45.455 1.29 0.00 0.00 4.35
878 1206 3.181480 TGACTTTTTGCCACCACTTAAGC 60.181 43.478 1.29 0.00 0.00 3.09
879 1207 4.647424 TGACTTTTTGCCACCACTTAAG 57.353 40.909 0.00 0.00 0.00 1.85
880 1208 5.407407 TTTGACTTTTTGCCACCACTTAA 57.593 34.783 0.00 0.00 0.00 1.85
881 1209 5.407407 TTTTGACTTTTTGCCACCACTTA 57.593 34.783 0.00 0.00 0.00 2.24
882 1210 3.971245 TTTGACTTTTTGCCACCACTT 57.029 38.095 0.00 0.00 0.00 3.16
883 1211 3.971245 TTTTGACTTTTTGCCACCACT 57.029 38.095 0.00 0.00 0.00 4.00
884 1212 3.126171 GGTTTTTGACTTTTTGCCACCAC 59.874 43.478 0.00 0.00 0.00 4.16
885 1213 3.339141 GGTTTTTGACTTTTTGCCACCA 58.661 40.909 0.00 0.00 0.00 4.17
886 1214 2.680841 GGGTTTTTGACTTTTTGCCACC 59.319 45.455 0.00 0.00 0.00 4.61
887 1215 2.680841 GGGGTTTTTGACTTTTTGCCAC 59.319 45.455 0.00 0.00 0.00 5.01
888 1216 2.678190 CGGGGTTTTTGACTTTTTGCCA 60.678 45.455 0.00 0.00 0.00 4.92
889 1217 1.937223 CGGGGTTTTTGACTTTTTGCC 59.063 47.619 0.00 0.00 0.00 4.52
890 1218 2.605818 GTCGGGGTTTTTGACTTTTTGC 59.394 45.455 0.00 0.00 0.00 3.68
891 1219 3.851098 TGTCGGGGTTTTTGACTTTTTG 58.149 40.909 0.00 0.00 33.81 2.44
892 1220 4.746535 ATGTCGGGGTTTTTGACTTTTT 57.253 36.364 0.00 0.00 33.81 1.94
893 1221 4.081365 ACAATGTCGGGGTTTTTGACTTTT 60.081 37.500 0.00 0.00 33.81 2.27
894 1222 3.449377 ACAATGTCGGGGTTTTTGACTTT 59.551 39.130 0.00 0.00 33.81 2.66
895 1223 3.028130 ACAATGTCGGGGTTTTTGACTT 58.972 40.909 0.00 0.00 33.81 3.01
896 1224 2.360801 CACAATGTCGGGGTTTTTGACT 59.639 45.455 0.00 0.00 33.81 3.41
897 1225 2.544903 CCACAATGTCGGGGTTTTTGAC 60.545 50.000 0.00 0.00 0.00 3.18
898 1226 1.683917 CCACAATGTCGGGGTTTTTGA 59.316 47.619 0.00 0.00 0.00 2.69
899 1227 1.270041 CCCACAATGTCGGGGTTTTTG 60.270 52.381 11.49 0.00 38.95 2.44
900 1228 1.044611 CCCACAATGTCGGGGTTTTT 58.955 50.000 11.49 0.00 38.95 1.94
901 1229 2.740121 CCCACAATGTCGGGGTTTT 58.260 52.632 11.49 0.00 38.95 2.43
902 1230 4.511838 CCCACAATGTCGGGGTTT 57.488 55.556 11.49 0.00 38.95 3.27
907 1235 1.209504 AGTATGGACCCACAATGTCGG 59.790 52.381 0.00 0.00 33.46 4.79
908 1236 2.550978 GAGTATGGACCCACAATGTCG 58.449 52.381 0.00 0.00 33.46 4.35
956 1284 0.824182 AGCGTCTCGAAGGATAGGGG 60.824 60.000 0.00 0.00 0.00 4.79
957 1285 0.312416 CAGCGTCTCGAAGGATAGGG 59.688 60.000 0.00 0.00 0.00 3.53
958 1286 0.318275 GCAGCGTCTCGAAGGATAGG 60.318 60.000 0.00 0.00 0.00 2.57
1093 1421 0.811616 GTCTGCTTACATCAGCCGGG 60.812 60.000 2.18 0.00 39.25 5.73
1099 1427 2.428530 AGATGCGAGTCTGCTTACATCA 59.571 45.455 0.00 0.00 38.61 3.07
1138 1467 1.826385 CAGAGGAAACCTGCGGAAAT 58.174 50.000 0.00 0.00 31.76 2.17
1145 1474 1.558756 AGATCTGGCAGAGGAAACCTG 59.441 52.381 23.24 0.00 31.76 4.00
1185 1515 3.497031 GTTGCCTCCGCCGCTTAC 61.497 66.667 0.00 0.00 0.00 2.34
1231 1561 1.480545 CACCCACATCACCGATACTGA 59.519 52.381 0.00 0.00 0.00 3.41
1250 1580 2.046411 AATGTCACCGCCGCATCA 60.046 55.556 0.00 0.00 0.00 3.07
1272 1602 2.352651 TGCATTCGCTCTGCAAATCTAC 59.647 45.455 4.25 0.00 46.06 2.59
1297 1627 4.129737 GCGCCGACAGAGCCACTA 62.130 66.667 0.00 0.00 0.00 2.74
1367 1697 5.347620 ACAAATGTGGCGTATACCTCTTA 57.652 39.130 0.00 0.00 0.00 2.10
1428 1758 7.995289 AGATCGATATGATACATGAGGAGAAC 58.005 38.462 0.00 0.00 37.47 3.01
1431 1763 8.022550 GCATAGATCGATATGATACATGAGGAG 58.977 40.741 11.54 0.00 37.47 3.69
1670 2004 5.091261 ACAGTGTCAGTTTTCTTCTCAGT 57.909 39.130 0.00 0.00 0.00 3.41
1768 2102 4.642489 ATCTTACCCCAAATCCCCAATT 57.358 40.909 0.00 0.00 0.00 2.32
1772 2106 3.817931 GCCATATCTTACCCCAAATCCCC 60.818 52.174 0.00 0.00 0.00 4.81
1773 2107 3.181423 TGCCATATCTTACCCCAAATCCC 60.181 47.826 0.00 0.00 0.00 3.85
1877 2211 0.104487 CTGCCATTGCCACACAACAA 59.896 50.000 0.00 0.00 42.27 2.83
1994 2333 2.039879 AGTCCGGGTGTTGCTTTTCTAT 59.960 45.455 0.00 0.00 0.00 1.98
1995 2334 1.418637 AGTCCGGGTGTTGCTTTTCTA 59.581 47.619 0.00 0.00 0.00 2.10
2108 2447 4.724399 TCTTGCCACACTTCTCCATTAAA 58.276 39.130 0.00 0.00 0.00 1.52
2127 2466 0.243095 GACGGCGAGTACACCTTCTT 59.757 55.000 16.62 0.00 0.00 2.52
2189 2528 8.199449 CCAATGCTATTGTTATTTTCATGGAGT 58.801 33.333 0.00 0.00 0.00 3.85
2194 2533 7.496591 CCTTGCCAATGCTATTGTTATTTTCAT 59.503 33.333 7.71 0.00 38.71 2.57
2234 2573 6.294010 GGACATTGAACCAAAGAAACTACTCC 60.294 42.308 0.00 0.00 0.00 3.85
2236 2575 6.126409 TGGACATTGAACCAAAGAAACTACT 58.874 36.000 5.25 0.00 32.93 2.57
2273 2612 0.250727 CCCCCTCAACGCTCTTTTGA 60.251 55.000 0.00 0.00 0.00 2.69
2351 2690 0.753479 TGCTCCCAACTCGGCAAAAA 60.753 50.000 0.00 0.00 0.00 1.94
2401 2740 0.900182 ATGCGGCTATCCTCATCCGA 60.900 55.000 0.00 0.00 44.23 4.55
2442 2781 4.113815 TGGGCCCTGCTTGATCCG 62.114 66.667 25.70 0.00 0.00 4.18
2552 2891 7.721286 CCAAATATCATGGTCTAGAAGTGTC 57.279 40.000 0.00 0.00 33.08 3.67
2589 2928 3.531538 AGTCTCGACTGTCTCATCTCTC 58.468 50.000 6.21 0.00 40.75 3.20
2600 2939 2.224066 ACCCACTGAAAAGTCTCGACTG 60.224 50.000 0.00 0.00 41.58 3.51


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

AutoCloner maintained by Alex Coulton.