Multiple sequence alignment - TraesCS7B01G165900

Loading Multiple Alignment...

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 TraesCS7B01G165900 chr7B 100.000 3060 0 0 1 3060 228813597 228810538 0.000000e+00 5651.0
1 TraesCS7B01G165900 chr7B 98.630 949 12 1 1 948 506625276 506626224 0.000000e+00 1679.0
2 TraesCS7B01G165900 chr7B 95.910 978 25 6 2088 3060 651499769 651498802 0.000000e+00 1570.0
3 TraesCS7B01G165900 chr7B 96.859 764 19 2 2297 3060 692389074 692389832 0.000000e+00 1273.0
4 TraesCS7B01G165900 chr7B 97.030 202 6 0 945 1146 506631791 506631992 1.050000e-89 340.0
5 TraesCS7B01G165900 chr7B 80.042 471 68 16 1162 1619 139634411 139633954 2.940000e-85 326.0
6 TraesCS7B01G165900 chr7B 94.009 217 8 1 2088 2299 43650033 43649817 1.060000e-84 324.0
7 TraesCS7B01G165900 chr7B 83.838 99 13 3 1050 1146 184985437 184985534 1.170000e-14 91.6
8 TraesCS7B01G165900 chr2B 98.841 949 3 2 1 948 556686140 556685199 0.000000e+00 1685.0
9 TraesCS7B01G165900 chr2B 96.429 980 23 4 2088 3060 404405307 404406281 0.000000e+00 1605.0
10 TraesCS7B01G165900 chr2B 97.775 764 14 1 2297 3060 770721273 770722033 0.000000e+00 1314.0
11 TraesCS7B01G165900 chr2B 98.571 210 2 1 945 1154 556680894 556680686 1.340000e-98 370.0
12 TraesCS7B01G165900 chr2A 94.521 949 48 4 1 948 480337429 480338374 0.000000e+00 1461.0
13 TraesCS7B01G165900 chr2A 94.437 773 33 6 2290 3059 736989440 736988675 0.000000e+00 1181.0
14 TraesCS7B01G165900 chr2A 90.794 554 44 4 1 551 641083287 641083836 0.000000e+00 734.0
15 TraesCS7B01G165900 chr2A 96.517 201 7 0 945 1145 480375157 480375357 1.760000e-87 333.0
16 TraesCS7B01G165900 chr5B 97.513 764 17 1 2297 3060 45196853 45196092 0.000000e+00 1304.0
17 TraesCS7B01G165900 chr5B 82.857 105 11 4 1046 1146 629602860 629602759 1.510000e-13 87.9
18 TraesCS7B01G165900 chr4B 97.251 764 18 1 2297 3060 22831447 22830687 0.000000e+00 1291.0
19 TraesCS7B01G165900 chr1B 96.990 764 18 2 2297 3060 52618457 52619215 0.000000e+00 1279.0
20 TraesCS7B01G165900 chr1B 94.466 777 31 5 2290 3060 519528361 519529131 0.000000e+00 1186.0
21 TraesCS7B01G165900 chr1B 95.475 221 2 3 2086 2299 171263593 171263374 2.260000e-91 346.0
22 TraesCS7B01G165900 chr1B 94.470 217 7 1 2088 2299 234126643 234126427 2.270000e-86 329.0
23 TraesCS7B01G165900 chr1B 83.838 99 11 4 1050 1145 15891842 15891938 4.200000e-14 89.8
24 TraesCS7B01G165900 chr7A 92.956 866 43 10 1152 2002 269138096 269138958 0.000000e+00 1245.0
25 TraesCS7B01G165900 chr7A 80.657 548 81 11 1159 1693 176990282 176989747 4.750000e-108 401.0
26 TraesCS7B01G165900 chr7A 94.419 215 5 2 2090 2299 21023065 21022853 1.060000e-84 324.0
27 TraesCS7B01G165900 chr7A 83.146 89 12 3 1914 2001 709144467 709144553 9.100000e-11 78.7
28 TraesCS7B01G165900 chr3B 96.078 765 25 3 2297 3060 797631900 797632660 0.000000e+00 1242.0
29 TraesCS7B01G165900 chr3B 95.090 774 26 6 2290 3060 541087234 541086470 0.000000e+00 1208.0
30 TraesCS7B01G165900 chr3B 93.392 227 8 2 2080 2299 817080848 817081074 2.270000e-86 329.0
31 TraesCS7B01G165900 chr4A 95.478 774 25 4 2290 3060 547072842 547073608 0.000000e+00 1227.0
32 TraesCS7B01G165900 chr2D 95.220 774 27 6 2290 3060 72958974 72958208 0.000000e+00 1216.0
33 TraesCS7B01G165900 chr6D 93.141 554 31 4 1 551 315634086 315633537 0.000000e+00 806.0
34 TraesCS7B01G165900 chr6D 88.942 208 22 1 740 947 86947228 86947022 3.920000e-64 255.0
35 TraesCS7B01G165900 chr7D 89.767 430 28 6 1331 1760 252051504 252051091 1.250000e-148 536.0
36 TraesCS7B01G165900 chr7D 85.294 340 19 11 1763 2071 252035505 252035166 3.810000e-84 322.0
37 TraesCS7B01G165900 chr7D 81.416 113 14 4 1046 1154 196998414 196998523 5.440000e-13 86.1
38 TraesCS7B01G165900 chr6B 92.544 228 8 3 2081 2299 151604531 151604304 4.920000e-83 318.0
39 TraesCS7B01G165900 chr6B 88.517 209 23 1 739 947 164862665 164862458 5.060000e-63 252.0
40 TraesCS7B01G165900 chr3A 91.525 236 8 6 2075 2299 391890963 391891197 6.370000e-82 315.0
41 TraesCS7B01G165900 chr6A 80.147 136 19 5 1016 1146 606073238 606073370 9.030000e-16 95.3
42 TraesCS7B01G165900 chr3D 82.857 105 11 4 1046 1146 289590669 289590568 1.510000e-13 87.9
43 TraesCS7B01G165900 chr5D 82.432 74 11 2 1922 1995 436985255 436985326 2.550000e-06 63.9
44 TraesCS7B01G165900 chr5A 97.222 36 1 0 1960 1995 552277673 552277708 9.160000e-06 62.1


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 TraesCS7B01G165900 chr7B 228810538 228813597 3059 True 5651 5651 100.000 1 3060 1 chr7B.!!$R3 3059
1 TraesCS7B01G165900 chr7B 506625276 506626224 948 False 1679 1679 98.630 1 948 1 chr7B.!!$F2 947
2 TraesCS7B01G165900 chr7B 651498802 651499769 967 True 1570 1570 95.910 2088 3060 1 chr7B.!!$R4 972
3 TraesCS7B01G165900 chr7B 692389074 692389832 758 False 1273 1273 96.859 2297 3060 1 chr7B.!!$F4 763
4 TraesCS7B01G165900 chr2B 556685199 556686140 941 True 1685 1685 98.841 1 948 1 chr2B.!!$R2 947
5 TraesCS7B01G165900 chr2B 404405307 404406281 974 False 1605 1605 96.429 2088 3060 1 chr2B.!!$F1 972
6 TraesCS7B01G165900 chr2B 770721273 770722033 760 False 1314 1314 97.775 2297 3060 1 chr2B.!!$F2 763
7 TraesCS7B01G165900 chr2A 480337429 480338374 945 False 1461 1461 94.521 1 948 1 chr2A.!!$F1 947
8 TraesCS7B01G165900 chr2A 736988675 736989440 765 True 1181 1181 94.437 2290 3059 1 chr2A.!!$R1 769
9 TraesCS7B01G165900 chr2A 641083287 641083836 549 False 734 734 90.794 1 551 1 chr2A.!!$F3 550
10 TraesCS7B01G165900 chr5B 45196092 45196853 761 True 1304 1304 97.513 2297 3060 1 chr5B.!!$R1 763
11 TraesCS7B01G165900 chr4B 22830687 22831447 760 True 1291 1291 97.251 2297 3060 1 chr4B.!!$R1 763
12 TraesCS7B01G165900 chr1B 52618457 52619215 758 False 1279 1279 96.990 2297 3060 1 chr1B.!!$F2 763
13 TraesCS7B01G165900 chr1B 519528361 519529131 770 False 1186 1186 94.466 2290 3060 1 chr1B.!!$F3 770
14 TraesCS7B01G165900 chr7A 269138096 269138958 862 False 1245 1245 92.956 1152 2002 1 chr7A.!!$F1 850
15 TraesCS7B01G165900 chr7A 176989747 176990282 535 True 401 401 80.657 1159 1693 1 chr7A.!!$R2 534
16 TraesCS7B01G165900 chr3B 797631900 797632660 760 False 1242 1242 96.078 2297 3060 1 chr3B.!!$F1 763
17 TraesCS7B01G165900 chr3B 541086470 541087234 764 True 1208 1208 95.090 2290 3060 1 chr3B.!!$R1 770
18 TraesCS7B01G165900 chr4A 547072842 547073608 766 False 1227 1227 95.478 2290 3060 1 chr4A.!!$F1 770
19 TraesCS7B01G165900 chr2D 72958208 72958974 766 True 1216 1216 95.220 2290 3060 1 chr2D.!!$R1 770
20 TraesCS7B01G165900 chr6D 315633537 315634086 549 True 806 806 93.141 1 551 1 chr6D.!!$R2 550

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
958 964 2.029623 ACTGCATGAATCATTGCTCCC 58.97 47.619 15.01 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 2223 0.033011 TCGGAAAGAGGGAGGGAGAG 60.033 60.0 0.0 0.0 0.0 3.2 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
894 900 3.295973 AGTTGCTTCCTAAACTTTGCCA 58.704 40.909 0.00 0.00 32.75 4.92
921 927 7.211573 TCACAATGGTAGAAAACTAAGTTCGA 58.788 34.615 0.00 0.00 0.00 3.71
948 954 4.081406 TGCTGGTTTCTTACTGCATGAAT 58.919 39.130 0.00 0.00 33.65 2.57
949 955 4.156556 TGCTGGTTTCTTACTGCATGAATC 59.843 41.667 0.00 0.00 33.65 2.52
950 956 4.156556 GCTGGTTTCTTACTGCATGAATCA 59.843 41.667 0.00 0.00 0.00 2.57
951 957 5.163581 GCTGGTTTCTTACTGCATGAATCAT 60.164 40.000 0.00 0.00 0.00 2.45
952 958 6.626623 GCTGGTTTCTTACTGCATGAATCATT 60.627 38.462 0.00 0.00 0.00 2.57
953 959 6.623486 TGGTTTCTTACTGCATGAATCATTG 58.377 36.000 0.00 0.00 0.00 2.82
954 960 5.517770 GGTTTCTTACTGCATGAATCATTGC 59.482 40.000 0.00 9.60 0.00 3.56
955 961 6.327934 GTTTCTTACTGCATGAATCATTGCT 58.672 36.000 15.01 3.37 0.00 3.91
956 962 5.746307 TCTTACTGCATGAATCATTGCTC 57.254 39.130 15.01 0.00 0.00 4.26
957 963 4.577693 TCTTACTGCATGAATCATTGCTCC 59.422 41.667 15.01 0.00 0.00 4.70
958 964 2.029623 ACTGCATGAATCATTGCTCCC 58.970 47.619 15.01 0.00 0.00 4.30
959 965 2.307768 CTGCATGAATCATTGCTCCCT 58.692 47.619 15.01 0.00 0.00 4.20
960 966 3.117776 ACTGCATGAATCATTGCTCCCTA 60.118 43.478 15.01 0.00 0.00 3.53
961 967 4.079970 CTGCATGAATCATTGCTCCCTAT 58.920 43.478 15.01 0.00 0.00 2.57
962 968 3.824443 TGCATGAATCATTGCTCCCTATG 59.176 43.478 15.01 0.00 0.00 2.23
963 969 3.825014 GCATGAATCATTGCTCCCTATGT 59.175 43.478 0.00 0.00 0.00 2.29
964 970 5.005740 GCATGAATCATTGCTCCCTATGTA 58.994 41.667 0.00 0.00 0.00 2.29
965 971 5.651139 GCATGAATCATTGCTCCCTATGTAT 59.349 40.000 0.00 0.00 0.00 2.29
966 972 6.825213 GCATGAATCATTGCTCCCTATGTATA 59.175 38.462 0.00 0.00 0.00 1.47
967 973 7.337689 GCATGAATCATTGCTCCCTATGTATAA 59.662 37.037 0.00 0.00 0.00 0.98
968 974 9.234827 CATGAATCATTGCTCCCTATGTATAAA 57.765 33.333 0.00 0.00 0.00 1.40
969 975 9.986157 ATGAATCATTGCTCCCTATGTATAAAT 57.014 29.630 0.00 0.00 0.00 1.40
970 976 9.453572 TGAATCATTGCTCCCTATGTATAAATC 57.546 33.333 0.00 0.00 0.00 2.17
971 977 8.498054 AATCATTGCTCCCTATGTATAAATCG 57.502 34.615 0.00 0.00 0.00 3.34
972 978 5.874810 TCATTGCTCCCTATGTATAAATCGC 59.125 40.000 0.00 0.00 0.00 4.58
973 979 4.202245 TGCTCCCTATGTATAAATCGCC 57.798 45.455 0.00 0.00 0.00 5.54
974 980 3.580895 TGCTCCCTATGTATAAATCGCCA 59.419 43.478 0.00 0.00 0.00 5.69
975 981 4.225042 TGCTCCCTATGTATAAATCGCCAT 59.775 41.667 0.00 0.00 0.00 4.40
976 982 5.423931 TGCTCCCTATGTATAAATCGCCATA 59.576 40.000 0.00 0.00 0.00 2.74
977 983 6.099701 TGCTCCCTATGTATAAATCGCCATAT 59.900 38.462 0.00 0.00 0.00 1.78
978 984 6.992715 GCTCCCTATGTATAAATCGCCATATT 59.007 38.462 0.00 0.00 0.00 1.28
979 985 7.041780 GCTCCCTATGTATAAATCGCCATATTG 60.042 40.741 0.00 0.00 0.00 1.90
980 986 7.857456 TCCCTATGTATAAATCGCCATATTGT 58.143 34.615 0.00 0.00 0.00 2.71
981 987 8.983789 TCCCTATGTATAAATCGCCATATTGTA 58.016 33.333 0.00 0.00 0.00 2.41
982 988 9.607988 CCCTATGTATAAATCGCCATATTGTAA 57.392 33.333 0.00 0.00 0.00 2.41
991 997 8.994429 AAATCGCCATATTGTAATTTTTGTCA 57.006 26.923 0.00 0.00 0.00 3.58
992 998 8.994429 AATCGCCATATTGTAATTTTTGTCAA 57.006 26.923 0.00 0.00 0.00 3.18
993 999 7.804614 TCGCCATATTGTAATTTTTGTCAAC 57.195 32.000 0.00 0.00 0.00 3.18
994 1000 7.598278 TCGCCATATTGTAATTTTTGTCAACT 58.402 30.769 0.00 0.00 0.00 3.16
995 1001 8.085296 TCGCCATATTGTAATTTTTGTCAACTT 58.915 29.630 0.00 0.00 0.00 2.66
996 1002 9.347934 CGCCATATTGTAATTTTTGTCAACTTA 57.652 29.630 0.00 0.00 0.00 2.24
1008 1014 9.762933 ATTTTTGTCAACTTATACATTGCAAGT 57.237 25.926 4.94 6.05 34.03 3.16
1009 1015 8.572828 TTTTGTCAACTTATACATTGCAAGTG 57.427 30.769 4.94 6.32 32.96 3.16
1010 1016 7.503521 TTGTCAACTTATACATTGCAAGTGA 57.496 32.000 4.94 0.00 32.96 3.41
1011 1017 7.503521 TGTCAACTTATACATTGCAAGTGAA 57.496 32.000 4.94 2.54 32.96 3.18
1012 1018 7.584108 TGTCAACTTATACATTGCAAGTGAAG 58.416 34.615 4.94 12.53 32.96 3.02
1013 1019 7.228507 TGTCAACTTATACATTGCAAGTGAAGT 59.771 33.333 4.94 13.06 32.96 3.01
1014 1020 8.717821 GTCAACTTATACATTGCAAGTGAAGTA 58.282 33.333 19.35 12.42 32.96 2.24
1015 1021 9.278978 TCAACTTATACATTGCAAGTGAAGTAA 57.721 29.630 19.35 13.45 32.96 2.24
1016 1022 9.891828 CAACTTATACATTGCAAGTGAAGTAAA 57.108 29.630 19.35 9.61 32.96 2.01
1052 1058 9.912634 TTTTCTGATTGTATTGGTCATCTTTTC 57.087 29.630 0.00 0.00 0.00 2.29
1053 1059 8.868522 TTCTGATTGTATTGGTCATCTTTTCT 57.131 30.769 0.00 0.00 0.00 2.52
1054 1060 9.958180 TTCTGATTGTATTGGTCATCTTTTCTA 57.042 29.630 0.00 0.00 0.00 2.10
1060 1066 8.642908 TGTATTGGTCATCTTTTCTATACACG 57.357 34.615 0.00 0.00 0.00 4.49
1061 1067 6.604735 ATTGGTCATCTTTTCTATACACGC 57.395 37.500 0.00 0.00 0.00 5.34
1062 1068 5.079689 TGGTCATCTTTTCTATACACGCA 57.920 39.130 0.00 0.00 0.00 5.24
1063 1069 5.670485 TGGTCATCTTTTCTATACACGCAT 58.330 37.500 0.00 0.00 0.00 4.73
1064 1070 6.811954 TGGTCATCTTTTCTATACACGCATA 58.188 36.000 0.00 0.00 0.00 3.14
1065 1071 7.269316 TGGTCATCTTTTCTATACACGCATAA 58.731 34.615 0.00 0.00 0.00 1.90
1066 1072 7.766738 TGGTCATCTTTTCTATACACGCATAAA 59.233 33.333 0.00 0.00 0.00 1.40
1067 1073 8.774586 GGTCATCTTTTCTATACACGCATAAAT 58.225 33.333 0.00 0.00 0.00 1.40
1072 1078 9.982291 TCTTTTCTATACACGCATAAATTTGAC 57.018 29.630 0.00 0.00 0.00 3.18
1073 1079 9.767684 CTTTTCTATACACGCATAAATTTGACA 57.232 29.630 0.00 0.00 0.00 3.58
1075 1081 9.715123 TTTCTATACACGCATAAATTTGACATG 57.285 29.630 0.00 0.00 0.00 3.21
1076 1082 7.351981 TCTATACACGCATAAATTTGACATGC 58.648 34.615 12.48 12.48 41.29 4.06
1077 1083 4.171663 ACACGCATAAATTTGACATGCA 57.828 36.364 19.38 0.00 44.19 3.96
1078 1084 4.746729 ACACGCATAAATTTGACATGCAT 58.253 34.783 19.38 6.27 44.19 3.96
1079 1085 5.170021 ACACGCATAAATTTGACATGCATT 58.830 33.333 19.38 7.22 44.19 3.56
1080 1086 6.328714 ACACGCATAAATTTGACATGCATTA 58.671 32.000 19.38 0.00 44.19 1.90
1081 1087 6.979817 ACACGCATAAATTTGACATGCATTAT 59.020 30.769 19.38 0.00 44.19 1.28
1082 1088 8.134261 ACACGCATAAATTTGACATGCATTATA 58.866 29.630 19.38 0.00 44.19 0.98
1083 1089 9.131416 CACGCATAAATTTGACATGCATTATAT 57.869 29.630 19.38 1.19 44.19 0.86
1084 1090 9.695526 ACGCATAAATTTGACATGCATTATATT 57.304 25.926 19.38 0.00 44.19 1.28
1110 1116 9.737427 TTATATATGCAACCAACAAAAATACGG 57.263 29.630 0.00 0.00 0.00 4.02
1111 1117 4.592485 ATGCAACCAACAAAAATACGGA 57.408 36.364 0.00 0.00 0.00 4.69
1112 1118 4.386867 TGCAACCAACAAAAATACGGAA 57.613 36.364 0.00 0.00 0.00 4.30
1113 1119 4.755411 TGCAACCAACAAAAATACGGAAA 58.245 34.783 0.00 0.00 0.00 3.13
1114 1120 5.360591 TGCAACCAACAAAAATACGGAAAT 58.639 33.333 0.00 0.00 0.00 2.17
1115 1121 5.235186 TGCAACCAACAAAAATACGGAAATG 59.765 36.000 0.00 0.00 0.00 2.32
1116 1122 5.674989 CAACCAACAAAAATACGGAAATGC 58.325 37.500 0.00 0.00 0.00 3.56
1117 1123 4.311606 ACCAACAAAAATACGGAAATGCC 58.688 39.130 0.00 0.00 0.00 4.40
1118 1124 3.682377 CCAACAAAAATACGGAAATGCCC 59.318 43.478 0.00 0.00 0.00 5.36
1140 1146 2.047655 CAACGCACGGGCCTTCTA 60.048 61.111 2.82 0.00 36.38 2.10
1141 1147 1.449601 CAACGCACGGGCCTTCTAT 60.450 57.895 2.82 0.00 36.38 1.98
1142 1148 1.024579 CAACGCACGGGCCTTCTATT 61.025 55.000 2.82 0.00 36.38 1.73
1143 1149 0.538118 AACGCACGGGCCTTCTATTA 59.462 50.000 2.82 0.00 36.38 0.98
1144 1150 0.104304 ACGCACGGGCCTTCTATTAG 59.896 55.000 2.82 0.00 36.38 1.73
1145 1151 0.104304 CGCACGGGCCTTCTATTAGT 59.896 55.000 2.82 0.00 36.38 2.24
1146 1152 1.867166 GCACGGGCCTTCTATTAGTC 58.133 55.000 0.00 0.00 0.00 2.59
1147 1153 1.868519 GCACGGGCCTTCTATTAGTCG 60.869 57.143 0.00 0.00 0.00 4.18
1148 1154 1.407979 CACGGGCCTTCTATTAGTCGT 59.592 52.381 0.84 0.00 0.00 4.34
1149 1155 2.620115 CACGGGCCTTCTATTAGTCGTA 59.380 50.000 0.84 0.00 0.00 3.43
1150 1156 2.883386 ACGGGCCTTCTATTAGTCGTAG 59.117 50.000 0.84 0.00 0.00 3.51
1355 1373 1.435925 CATGTACGCCTACGCCTCA 59.564 57.895 0.00 0.00 45.53 3.86
1356 1374 0.179121 CATGTACGCCTACGCCTCAA 60.179 55.000 0.00 0.00 45.53 3.02
1576 1594 4.008933 GCTCCTCGTGCTGTGGGT 62.009 66.667 0.00 0.00 0.00 4.51
1591 1609 2.970324 GGTGTGGCTTGTTCGCGA 60.970 61.111 3.71 3.71 0.00 5.87
1632 1650 2.547642 CCGTCGGGTAAAACTACAACCA 60.548 50.000 2.34 0.00 34.83 3.67
1666 1684 3.559171 GGAAACTCTATGCCCAAGACACA 60.559 47.826 0.00 0.00 0.00 3.72
1705 1724 0.878416 TACCGAAAGCATGTTGTGGC 59.122 50.000 0.00 0.00 0.00 5.01
1761 1780 2.738321 GCACCAAGTTCAAACAGGTTGG 60.738 50.000 0.00 9.59 42.89 3.77
1784 1803 3.547746 GTGAACACCAGGGAAAACTACA 58.452 45.455 0.00 0.00 0.00 2.74
1786 1805 2.651382 ACACCAGGGAAAACTACACC 57.349 50.000 0.00 0.00 0.00 4.16
1787 1806 1.847737 ACACCAGGGAAAACTACACCA 59.152 47.619 0.00 0.00 0.00 4.17
1788 1807 2.158667 ACACCAGGGAAAACTACACCAG 60.159 50.000 0.00 0.00 0.00 4.00
1789 1808 1.202891 ACCAGGGAAAACTACACCAGC 60.203 52.381 0.00 0.00 0.00 4.85
1790 1809 1.202879 CCAGGGAAAACTACACCAGCA 60.203 52.381 0.00 0.00 0.00 4.41
1791 1810 2.555227 CCAGGGAAAACTACACCAGCAT 60.555 50.000 0.00 0.00 0.00 3.79
1834 1853 4.133856 GTGTACATCACAAGTTCACAGC 57.866 45.455 0.00 0.00 45.51 4.40
1868 1887 5.337250 GCCGGGTTATCTCTTTTCCAAAAAT 60.337 40.000 2.18 0.00 0.00 1.82
1958 1989 2.356382 CAGGGTTGGCGCGAAAATATTA 59.644 45.455 12.10 0.00 0.00 0.98
2084 2116 8.764524 ATATAAATAGCAGAGCTCTTTTACGG 57.235 34.615 15.27 2.40 40.44 4.02
2085 2117 4.473477 AATAGCAGAGCTCTTTTACGGT 57.527 40.909 15.27 10.70 40.44 4.83
2086 2118 2.086054 AGCAGAGCTCTTTTACGGTG 57.914 50.000 15.27 1.82 30.62 4.94
2190 2222 3.274095 TCAAATCCTCACACACACACA 57.726 42.857 0.00 0.00 0.00 3.72
2191 2223 2.942376 TCAAATCCTCACACACACACAC 59.058 45.455 0.00 0.00 0.00 3.82
2206 2238 1.132689 ACACACTCTCCCTCCCTCTTT 60.133 52.381 0.00 0.00 0.00 2.52
2208 2240 1.199615 CACTCTCCCTCCCTCTTTCC 58.800 60.000 0.00 0.00 0.00 3.13
2252 2286 6.351371 CCCTCTCTCTAACACACACACATATT 60.351 42.308 0.00 0.00 0.00 1.28
2619 2661 2.492881 TGCGCATCATGAGGAACAATTT 59.507 40.909 12.39 0.00 0.00 1.82
2869 2917 7.667575 AGCAGATTGATTAAGGAACTCTAGA 57.332 36.000 0.00 0.00 38.49 2.43
2977 3029 3.407424 AGTTTACTGCTGCACATGAGA 57.593 42.857 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
894 900 8.504005 CGAACTTAGTTTTCTACCATTGTGAAT 58.496 33.333 0.00 0.00 31.46 2.57
921 927 4.144297 TGCAGTAAGAAACCAGCAAGAAT 58.856 39.130 0.00 0.00 36.88 2.40
948 954 5.874810 GCGATTTATACATAGGGAGCAATGA 59.125 40.000 0.00 0.00 0.00 2.57
949 955 5.065218 GGCGATTTATACATAGGGAGCAATG 59.935 44.000 0.00 0.00 0.00 2.82
950 956 5.186198 GGCGATTTATACATAGGGAGCAAT 58.814 41.667 0.00 0.00 0.00 3.56
951 957 4.041075 TGGCGATTTATACATAGGGAGCAA 59.959 41.667 0.00 0.00 0.00 3.91
952 958 3.580895 TGGCGATTTATACATAGGGAGCA 59.419 43.478 0.00 0.00 0.00 4.26
953 959 4.202245 TGGCGATTTATACATAGGGAGC 57.798 45.455 0.00 0.00 0.00 4.70
954 960 7.987458 ACAATATGGCGATTTATACATAGGGAG 59.013 37.037 0.00 0.00 30.25 4.30
955 961 7.857456 ACAATATGGCGATTTATACATAGGGA 58.143 34.615 0.00 0.00 30.25 4.20
956 962 9.607988 TTACAATATGGCGATTTATACATAGGG 57.392 33.333 0.00 0.00 30.25 3.53
966 972 8.994429 TGACAAAAATTACAATATGGCGATTT 57.006 26.923 0.00 0.00 0.00 2.17
967 973 8.868916 GTTGACAAAAATTACAATATGGCGATT 58.131 29.630 0.00 0.00 0.00 3.34
968 974 8.250332 AGTTGACAAAAATTACAATATGGCGAT 58.750 29.630 0.00 0.00 0.00 4.58
969 975 7.598278 AGTTGACAAAAATTACAATATGGCGA 58.402 30.769 0.00 0.00 0.00 5.54
970 976 7.810766 AGTTGACAAAAATTACAATATGGCG 57.189 32.000 0.00 0.00 0.00 5.69
982 988 9.762933 ACTTGCAATGTATAAGTTGACAAAAAT 57.237 25.926 0.00 0.00 30.98 1.82
983 989 9.029243 CACTTGCAATGTATAAGTTGACAAAAA 57.971 29.630 0.00 0.00 32.69 1.94
984 990 8.409371 TCACTTGCAATGTATAAGTTGACAAAA 58.591 29.630 0.00 0.00 32.69 2.44
985 991 7.935520 TCACTTGCAATGTATAAGTTGACAAA 58.064 30.769 0.00 0.00 32.69 2.83
986 992 7.503521 TCACTTGCAATGTATAAGTTGACAA 57.496 32.000 0.00 0.00 32.69 3.18
987 993 7.228507 ACTTCACTTGCAATGTATAAGTTGACA 59.771 33.333 0.00 0.00 32.69 3.58
988 994 7.584987 ACTTCACTTGCAATGTATAAGTTGAC 58.415 34.615 0.00 0.00 32.69 3.18
989 995 7.744087 ACTTCACTTGCAATGTATAAGTTGA 57.256 32.000 0.00 0.00 32.69 3.18
990 996 9.891828 TTTACTTCACTTGCAATGTATAAGTTG 57.108 29.630 20.69 4.68 33.96 3.16
1026 1032 9.912634 GAAAAGATGACCAATACAATCAGAAAA 57.087 29.630 0.00 0.00 0.00 2.29
1027 1033 9.300681 AGAAAAGATGACCAATACAATCAGAAA 57.699 29.630 0.00 0.00 0.00 2.52
1028 1034 8.868522 AGAAAAGATGACCAATACAATCAGAA 57.131 30.769 0.00 0.00 0.00 3.02
1034 1040 9.093970 CGTGTATAGAAAAGATGACCAATACAA 57.906 33.333 0.00 0.00 32.22 2.41
1035 1041 7.223971 GCGTGTATAGAAAAGATGACCAATACA 59.776 37.037 0.00 0.00 0.00 2.29
1036 1042 7.223971 TGCGTGTATAGAAAAGATGACCAATAC 59.776 37.037 0.00 0.00 0.00 1.89
1037 1043 7.269316 TGCGTGTATAGAAAAGATGACCAATA 58.731 34.615 0.00 0.00 0.00 1.90
1038 1044 6.112734 TGCGTGTATAGAAAAGATGACCAAT 58.887 36.000 0.00 0.00 0.00 3.16
1039 1045 5.483811 TGCGTGTATAGAAAAGATGACCAA 58.516 37.500 0.00 0.00 0.00 3.67
1040 1046 5.079689 TGCGTGTATAGAAAAGATGACCA 57.920 39.130 0.00 0.00 0.00 4.02
1041 1047 7.709269 TTATGCGTGTATAGAAAAGATGACC 57.291 36.000 0.00 0.00 0.00 4.02
1046 1052 9.982291 GTCAAATTTATGCGTGTATAGAAAAGA 57.018 29.630 0.00 0.00 0.00 2.52
1047 1053 9.767684 TGTCAAATTTATGCGTGTATAGAAAAG 57.232 29.630 0.00 0.00 0.00 2.27
1049 1055 9.715123 CATGTCAAATTTATGCGTGTATAGAAA 57.285 29.630 0.00 0.00 0.00 2.52
1050 1056 7.855409 GCATGTCAAATTTATGCGTGTATAGAA 59.145 33.333 8.29 0.00 37.97 2.10
1051 1057 7.351981 GCATGTCAAATTTATGCGTGTATAGA 58.648 34.615 8.29 0.00 37.97 1.98
1052 1058 7.538981 GCATGTCAAATTTATGCGTGTATAG 57.461 36.000 8.29 0.00 37.97 1.31
1084 1090 9.737427 CCGTATTTTTGTTGGTTGCATATATAA 57.263 29.630 0.00 0.00 0.00 0.98
1085 1091 9.121658 TCCGTATTTTTGTTGGTTGCATATATA 57.878 29.630 0.00 0.00 0.00 0.86
1086 1092 8.001881 TCCGTATTTTTGTTGGTTGCATATAT 57.998 30.769 0.00 0.00 0.00 0.86
1087 1093 7.392494 TCCGTATTTTTGTTGGTTGCATATA 57.608 32.000 0.00 0.00 0.00 0.86
1088 1094 6.274157 TCCGTATTTTTGTTGGTTGCATAT 57.726 33.333 0.00 0.00 0.00 1.78
1089 1095 5.707242 TCCGTATTTTTGTTGGTTGCATA 57.293 34.783 0.00 0.00 0.00 3.14
1090 1096 4.592485 TCCGTATTTTTGTTGGTTGCAT 57.408 36.364 0.00 0.00 0.00 3.96
1091 1097 4.386867 TTCCGTATTTTTGTTGGTTGCA 57.613 36.364 0.00 0.00 0.00 4.08
1092 1098 5.674989 CATTTCCGTATTTTTGTTGGTTGC 58.325 37.500 0.00 0.00 0.00 4.17
1093 1099 5.333721 GGCATTTCCGTATTTTTGTTGGTTG 60.334 40.000 0.00 0.00 0.00 3.77
1094 1100 4.752604 GGCATTTCCGTATTTTTGTTGGTT 59.247 37.500 0.00 0.00 0.00 3.67
1095 1101 4.311606 GGCATTTCCGTATTTTTGTTGGT 58.688 39.130 0.00 0.00 0.00 3.67
1096 1102 3.682377 GGGCATTTCCGTATTTTTGTTGG 59.318 43.478 0.00 0.00 34.94 3.77
1097 1103 3.366422 CGGGCATTTCCGTATTTTTGTTG 59.634 43.478 0.00 0.00 44.60 3.33
1098 1104 3.580731 CGGGCATTTCCGTATTTTTGTT 58.419 40.909 0.00 0.00 44.60 2.83
1099 1105 3.224884 CGGGCATTTCCGTATTTTTGT 57.775 42.857 0.00 0.00 44.60 2.83
1123 1129 1.024579 AATAGAAGGCCCGTGCGTTG 61.025 55.000 1.72 0.00 45.01 4.10
1125 1131 0.104304 CTAATAGAAGGCCCGTGCGT 59.896 55.000 0.00 0.00 38.85 5.24
1126 1132 0.104304 ACTAATAGAAGGCCCGTGCG 59.896 55.000 0.00 0.00 38.85 5.34
1127 1133 1.867166 GACTAATAGAAGGCCCGTGC 58.133 55.000 0.00 0.00 0.00 5.34
1128 1134 1.407979 ACGACTAATAGAAGGCCCGTG 59.592 52.381 0.00 0.00 0.00 4.94
1129 1135 1.772836 ACGACTAATAGAAGGCCCGT 58.227 50.000 0.00 0.00 0.00 5.28
1130 1136 2.228343 CCTACGACTAATAGAAGGCCCG 59.772 54.545 0.00 0.00 0.00 6.13
1131 1137 3.229293 ACCTACGACTAATAGAAGGCCC 58.771 50.000 0.00 0.00 0.00 5.80
1132 1138 4.458642 CCTACCTACGACTAATAGAAGGCC 59.541 50.000 0.00 0.00 0.00 5.19
1133 1139 5.069318 ACCTACCTACGACTAATAGAAGGC 58.931 45.833 0.00 0.00 31.04 4.35
1134 1140 6.367422 CGTACCTACCTACGACTAATAGAAGG 59.633 46.154 0.00 0.00 41.75 3.46
1135 1141 6.128688 GCGTACCTACCTACGACTAATAGAAG 60.129 46.154 3.02 0.00 41.75 2.85
1136 1142 5.696724 GCGTACCTACCTACGACTAATAGAA 59.303 44.000 3.02 0.00 41.75 2.10
1137 1143 5.221441 TGCGTACCTACCTACGACTAATAGA 60.221 44.000 3.02 0.00 41.75 1.98
1138 1144 4.991056 TGCGTACCTACCTACGACTAATAG 59.009 45.833 3.02 0.00 41.75 1.73
1139 1145 4.750098 GTGCGTACCTACCTACGACTAATA 59.250 45.833 3.02 0.00 41.75 0.98
1140 1146 3.561725 GTGCGTACCTACCTACGACTAAT 59.438 47.826 3.02 0.00 41.75 1.73
1141 1147 2.936498 GTGCGTACCTACCTACGACTAA 59.064 50.000 3.02 0.00 41.75 2.24
1142 1148 2.093711 TGTGCGTACCTACCTACGACTA 60.094 50.000 0.00 0.00 41.75 2.59
1143 1149 1.339055 TGTGCGTACCTACCTACGACT 60.339 52.381 0.00 0.00 41.75 4.18
1144 1150 1.086696 TGTGCGTACCTACCTACGAC 58.913 55.000 0.00 0.28 41.75 4.34
1145 1151 1.942657 GATGTGCGTACCTACCTACGA 59.057 52.381 0.00 0.00 41.75 3.43
1146 1152 1.002033 GGATGTGCGTACCTACCTACG 60.002 57.143 0.00 0.00 42.04 3.51
1147 1153 2.026641 TGGATGTGCGTACCTACCTAC 58.973 52.381 0.00 0.00 0.00 3.18
1148 1154 2.440517 TGGATGTGCGTACCTACCTA 57.559 50.000 0.00 0.00 0.00 3.08
1149 1155 1.412710 CATGGATGTGCGTACCTACCT 59.587 52.381 0.00 0.00 0.00 3.08
1150 1156 1.540363 CCATGGATGTGCGTACCTACC 60.540 57.143 5.56 2.71 0.00 3.18
1217 1229 1.303561 GGCCATGAACCAGAGCACA 60.304 57.895 0.00 0.00 0.00 4.57
1355 1373 0.706433 ACAGGATCAACAGGGCCATT 59.294 50.000 6.18 0.00 0.00 3.16
1356 1374 0.257039 GACAGGATCAACAGGGCCAT 59.743 55.000 6.18 0.00 0.00 4.40
1521 1539 2.671177 CGAGACAAGTGCAAGCCGG 61.671 63.158 0.00 0.00 0.00 6.13
1555 1573 3.241530 ACAGCACGAGGAGCCCAA 61.242 61.111 0.00 0.00 0.00 4.12
1576 1594 0.942410 GTACTCGCGAACAAGCCACA 60.942 55.000 11.33 0.00 0.00 4.17
1666 1684 1.153127 TTTTTCCAGACGCGTGGGT 60.153 52.632 20.70 0.00 38.26 4.51
1705 1724 3.398353 GAGACGCCGAGGTTCTCCG 62.398 68.421 10.15 0.00 39.05 4.63
1761 1780 1.037493 GTTTTCCCTGGTGTTCACCC 58.963 55.000 17.78 2.70 0.00 4.61
1779 1798 2.684881 GCAATTGCTATGCTGGTGTAGT 59.315 45.455 23.21 0.00 40.64 2.73
1780 1799 2.684374 TGCAATTGCTATGCTGGTGTAG 59.316 45.455 29.37 0.00 44.14 2.74
1781 1800 2.684374 CTGCAATTGCTATGCTGGTGTA 59.316 45.455 29.37 5.31 44.14 2.90
1782 1801 1.475280 CTGCAATTGCTATGCTGGTGT 59.525 47.619 29.37 0.00 44.14 4.16
1783 1802 2.203800 CTGCAATTGCTATGCTGGTG 57.796 50.000 29.37 6.34 44.14 4.17
1786 1805 3.513680 TTTCCTGCAATTGCTATGCTG 57.486 42.857 29.37 8.93 44.14 4.41
1787 1806 4.248058 GTTTTTCCTGCAATTGCTATGCT 58.752 39.130 29.37 0.00 44.14 3.79
1788 1807 3.371898 GGTTTTTCCTGCAATTGCTATGC 59.628 43.478 29.37 5.62 44.08 3.14
1789 1808 4.824289 AGGTTTTTCCTGCAATTGCTATG 58.176 39.130 29.37 18.79 46.19 2.23
1825 1844 0.534412 CCTCTCCATCGCTGTGAACT 59.466 55.000 0.00 0.00 0.00 3.01
1826 1845 1.086634 GCCTCTCCATCGCTGTGAAC 61.087 60.000 0.00 0.00 0.00 3.18
1834 1853 1.472662 ATAACCCGGCCTCTCCATCG 61.473 60.000 0.00 0.00 34.01 3.84
1893 1913 8.986477 ACTTTTGAGTAATTTGAATATGGCAC 57.014 30.769 0.00 0.00 0.00 5.01
2064 2096 4.081642 TCACCGTAAAAGAGCTCTGCTATT 60.082 41.667 19.06 12.57 42.09 1.73
2065 2097 3.447586 TCACCGTAAAAGAGCTCTGCTAT 59.552 43.478 19.06 6.53 39.88 2.97
2066 2098 2.823747 TCACCGTAAAAGAGCTCTGCTA 59.176 45.455 19.06 8.98 39.88 3.49
2067 2099 1.618837 TCACCGTAAAAGAGCTCTGCT 59.381 47.619 19.06 10.07 43.88 4.24
2068 2100 1.727335 GTCACCGTAAAAGAGCTCTGC 59.273 52.381 19.06 7.36 0.00 4.26
2069 2101 3.305398 AGTCACCGTAAAAGAGCTCTG 57.695 47.619 19.06 5.93 0.00 3.35
2070 2102 4.333690 TCTAGTCACCGTAAAAGAGCTCT 58.666 43.478 11.45 11.45 0.00 4.09
2071 2103 4.698583 TCTAGTCACCGTAAAAGAGCTC 57.301 45.455 5.27 5.27 0.00 4.09
2072 2104 4.765856 TCTTCTAGTCACCGTAAAAGAGCT 59.234 41.667 0.00 0.00 0.00 4.09
2073 2105 5.056894 TCTTCTAGTCACCGTAAAAGAGC 57.943 43.478 0.00 0.00 0.00 4.09
2074 2106 5.568296 CGTTCTTCTAGTCACCGTAAAAGAG 59.432 44.000 0.00 0.00 0.00 2.85
2075 2107 5.455392 CGTTCTTCTAGTCACCGTAAAAGA 58.545 41.667 0.00 0.00 0.00 2.52
2076 2108 4.089636 GCGTTCTTCTAGTCACCGTAAAAG 59.910 45.833 0.00 0.00 0.00 2.27
2077 2109 3.983344 GCGTTCTTCTAGTCACCGTAAAA 59.017 43.478 0.00 0.00 0.00 1.52
2078 2110 3.568538 GCGTTCTTCTAGTCACCGTAAA 58.431 45.455 0.00 0.00 0.00 2.01
2079 2111 2.095059 GGCGTTCTTCTAGTCACCGTAA 60.095 50.000 0.00 0.00 0.00 3.18
2080 2112 1.470098 GGCGTTCTTCTAGTCACCGTA 59.530 52.381 0.00 0.00 0.00 4.02
2081 2113 0.243095 GGCGTTCTTCTAGTCACCGT 59.757 55.000 0.00 0.00 0.00 4.83
2082 2114 0.458025 GGGCGTTCTTCTAGTCACCG 60.458 60.000 0.00 0.00 0.00 4.94
2083 2115 0.458025 CGGGCGTTCTTCTAGTCACC 60.458 60.000 0.00 0.00 0.00 4.02
2084 2116 0.243095 ACGGGCGTTCTTCTAGTCAC 59.757 55.000 0.00 0.00 0.00 3.67
2085 2117 0.242825 CACGGGCGTTCTTCTAGTCA 59.757 55.000 0.00 0.00 0.00 3.41
2086 2118 1.077089 GCACGGGCGTTCTTCTAGTC 61.077 60.000 0.00 0.00 0.00 2.59
2190 2222 0.324830 CGGAAAGAGGGAGGGAGAGT 60.325 60.000 0.00 0.00 0.00 3.24
2191 2223 0.033011 TCGGAAAGAGGGAGGGAGAG 60.033 60.000 0.00 0.00 0.00 3.20
2206 2238 1.619975 AGGGGGAGAGAGAGTCGGA 60.620 63.158 0.00 0.00 0.00 4.55
2208 2240 0.179029 GAGAGGGGGAGAGAGAGTCG 60.179 65.000 0.00 0.00 0.00 4.18
2252 2286 5.614831 TGGATTATGGTCCCCAATAAGATGA 59.385 40.000 0.00 0.00 36.95 2.92
2375 2414 1.798223 CTCGCGTGAGTGGAATTTTGA 59.202 47.619 17.90 0.00 43.13 2.69
2484 2526 0.322098 TCCATGCACCGAACCGATTT 60.322 50.000 0.00 0.00 0.00 2.17
2485 2527 0.107214 ATCCATGCACCGAACCGATT 60.107 50.000 0.00 0.00 0.00 3.34
2486 2528 0.815213 CATCCATGCACCGAACCGAT 60.815 55.000 0.00 0.00 0.00 4.18
2586 2628 2.933769 TGATGCGCAGATGTAGATACG 58.066 47.619 18.32 0.00 0.00 3.06
2588 2630 4.381292 CCTCATGATGCGCAGATGTAGATA 60.381 45.833 24.06 9.89 0.00 1.98
2679 2721 8.579006 CACCACGTGGGAAGTAATACTAATATA 58.421 37.037 36.47 0.00 41.15 0.86
2977 3029 2.553904 CCCTCTGCTTTGTGTGGATCTT 60.554 50.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.