Multiple sequence alignment - TraesCS6A01G203900

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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 TraesCS6A01G203900 chr6A 100.000 2644 0 0 1 2644 352513017 352510374 0.000000e+00 4883.0
1 TraesCS6A01G203900 chr6A 88.472 2663 275 25 1 2644 352520617 352517968 0.000000e+00 3188.0
2 TraesCS6A01G203900 chr6A 82.064 591 89 14 93 674 218019514 218020096 3.060000e-134 488.0
3 TraesCS6A01G203900 chr6A 85.246 122 10 4 1383 1503 302479031 302479145 4.620000e-23 119.0
4 TraesCS6A01G203900 chr6A 90.476 84 8 0 833 916 250996025 250996108 7.740000e-21 111.0
5 TraesCS6A01G203900 chr4A 86.448 974 110 17 1681 2644 338822875 338821914 0.000000e+00 1048.0
6 TraesCS6A01G203900 chr4A 87.500 136 17 0 1384 1519 404371829 404371694 9.800000e-35 158.0
7 TraesCS6A01G203900 chr2A 85.670 963 114 17 1681 2634 731074581 731073634 0.000000e+00 992.0
8 TraesCS6A01G203900 chr2A 84.979 972 127 15 1681 2644 279056831 279057791 0.000000e+00 968.0
9 TraesCS6A01G203900 chr2A 90.000 120 12 0 1383 1502 183580876 183580757 3.520000e-34 156.0
10 TraesCS6A01G203900 chr2A 88.333 120 14 0 1383 1502 180505987 180505868 7.630000e-31 145.0
11 TraesCS6A01G203900 chr2A 95.181 83 3 1 837 919 467789787 467789868 2.140000e-26 130.0
12 TraesCS6A01G203900 chr2A 92.105 76 6 0 842 917 332739656 332739731 1.000000e-19 108.0
13 TraesCS6A01G203900 chr2A 87.037 54 6 1 971 1024 486828749 486828697 2.840000e-05 60.2
14 TraesCS6A01G203900 chr7A 82.907 1135 155 30 1530 2642 393489812 393490929 0.000000e+00 985.0
15 TraesCS6A01G203900 chr7A 94.667 75 4 0 842 916 511396053 511395979 1.660000e-22 117.0
16 TraesCS6A01G203900 chr7A 88.000 75 9 0 1457 1531 574533027 574532953 3.620000e-14 89.8
17 TraesCS6A01G203900 chr7A 92.857 42 2 1 1464 1504 229469311 229469352 2.840000e-05 60.2
18 TraesCS6A01G203900 chr3D 85.333 975 117 23 1681 2644 221078280 221079239 0.000000e+00 985.0
19 TraesCS6A01G203900 chr4D 85.258 970 126 16 1681 2644 275920495 275919537 0.000000e+00 983.0
20 TraesCS6A01G203900 chr4D 88.679 53 6 0 962 1014 161356952 161356900 6.110000e-07 65.8
21 TraesCS6A01G203900 chr2D 84.852 977 117 27 1681 2644 347582631 347581673 0.000000e+00 955.0
22 TraesCS6A01G203900 chr2D 84.381 557 66 18 1 549 245522514 245523057 6.480000e-146 527.0
23 TraesCS6A01G203900 chr2D 86.792 53 6 1 959 1011 441434970 441435021 1.020000e-04 58.4
24 TraesCS6A01G203900 chr7D 83.414 1037 140 28 1621 2644 507488559 507489576 0.000000e+00 933.0
25 TraesCS6A01G203900 chr7B 81.537 1132 156 43 1530 2643 195494257 195495353 0.000000e+00 883.0
26 TraesCS6A01G203900 chr7B 85.252 556 61 18 1 549 273826316 273826857 1.070000e-153 553.0
27 TraesCS6A01G203900 chr7B 82.432 592 79 22 1 582 495910632 495910056 6.570000e-136 494.0
28 TraesCS6A01G203900 chr7B 86.667 195 24 2 829 1023 462313297 462313105 5.730000e-52 215.0
29 TraesCS6A01G203900 chr7B 88.535 157 17 1 675 831 440440402 440440247 3.470000e-44 189.0
30 TraesCS6A01G203900 chr4B 85.169 708 82 18 1 700 311419879 311420571 0.000000e+00 704.0
31 TraesCS6A01G203900 chr4B 82.776 598 79 21 1 589 446182395 446181813 1.820000e-141 512.0
32 TraesCS6A01G203900 chr4B 88.040 301 36 0 834 1134 579305408 579305108 9.000000e-95 357.0
33 TraesCS6A01G203900 chr4B 86.047 301 42 0 834 1134 409694234 409693934 9.130000e-85 324.0
34 TraesCS6A01G203900 chr4B 85.050 301 45 0 834 1134 409702259 409701959 9.190000e-80 307.0
35 TraesCS6A01G203900 chr4B 82.486 177 25 5 1380 1554 306320442 306320270 1.640000e-32 150.0
36 TraesCS6A01G203900 chr3B 82.040 696 85 29 8 679 480863218 480863897 8.270000e-155 556.0
37 TraesCS6A01G203900 chr3B 81.556 694 89 28 8 679 367754352 367753676 1.080000e-148 536.0
38 TraesCS6A01G203900 chr5A 88.430 121 14 0 1383 1503 153554595 153554715 2.120000e-31 147.0
39 TraesCS6A01G203900 chr6B 88.889 108 10 2 1380 1485 164500424 164500317 5.940000e-27 132.0
40 TraesCS6A01G203900 chr3A 89.524 105 9 2 1380 1483 332892190 332892293 5.940000e-27 132.0
41 TraesCS6A01G203900 chr1B 94.444 54 2 1 742 795 572602315 572602367 6.070000e-12 82.4


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 TraesCS6A01G203900 chr6A 352510374 352513017 2643 True 4883 4883 100.000 1 2644 1 chr6A.!!$R1 2643
1 TraesCS6A01G203900 chr6A 352517968 352520617 2649 True 3188 3188 88.472 1 2644 1 chr6A.!!$R2 2643
2 TraesCS6A01G203900 chr6A 218019514 218020096 582 False 488 488 82.064 93 674 1 chr6A.!!$F1 581
3 TraesCS6A01G203900 chr4A 338821914 338822875 961 True 1048 1048 86.448 1681 2644 1 chr4A.!!$R1 963
4 TraesCS6A01G203900 chr2A 731073634 731074581 947 True 992 992 85.670 1681 2634 1 chr2A.!!$R4 953
5 TraesCS6A01G203900 chr2A 279056831 279057791 960 False 968 968 84.979 1681 2644 1 chr2A.!!$F1 963
6 TraesCS6A01G203900 chr7A 393489812 393490929 1117 False 985 985 82.907 1530 2642 1 chr7A.!!$F2 1112
7 TraesCS6A01G203900 chr3D 221078280 221079239 959 False 985 985 85.333 1681 2644 1 chr3D.!!$F1 963
8 TraesCS6A01G203900 chr4D 275919537 275920495 958 True 983 983 85.258 1681 2644 1 chr4D.!!$R2 963
9 TraesCS6A01G203900 chr2D 347581673 347582631 958 True 955 955 84.852 1681 2644 1 chr2D.!!$R1 963
10 TraesCS6A01G203900 chr2D 245522514 245523057 543 False 527 527 84.381 1 549 1 chr2D.!!$F1 548
11 TraesCS6A01G203900 chr7D 507488559 507489576 1017 False 933 933 83.414 1621 2644 1 chr7D.!!$F1 1023
12 TraesCS6A01G203900 chr7B 195494257 195495353 1096 False 883 883 81.537 1530 2643 1 chr7B.!!$F1 1113
13 TraesCS6A01G203900 chr7B 273826316 273826857 541 False 553 553 85.252 1 549 1 chr7B.!!$F2 548
14 TraesCS6A01G203900 chr7B 495910056 495910632 576 True 494 494 82.432 1 582 1 chr7B.!!$R3 581
15 TraesCS6A01G203900 chr4B 311419879 311420571 692 False 704 704 85.169 1 700 1 chr4B.!!$F1 699
16 TraesCS6A01G203900 chr4B 446181813 446182395 582 True 512 512 82.776 1 589 1 chr4B.!!$R4 588
17 TraesCS6A01G203900 chr3B 480863218 480863897 679 False 556 556 82.040 8 679 1 chr3B.!!$F1 671
18 TraesCS6A01G203900 chr3B 367753676 367754352 676 True 536 536 81.556 8 679 1 chr3B.!!$R1 671

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
668 714 0.184933 CCATCCTCTCGGTCTCTCCT 59.815 60.0 0.00 0.0 0.0 3.69 F
1093 1139 0.038159 CCTCCAGGTCTGACAACGTC 60.038 60.0 10.38 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 1559 0.179067 TTGTTCACTCGACGGCCTTT 60.179 50.0 0.00 0.00 0.00 3.11 R
2604 2724 0.248377 AGGTAGCGCGACATAACGAC 60.248 55.0 22.25 2.95 35.09 4.34 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
39 40 5.466432 TCGTCGTGTGATTTGTTTTGTTA 57.534 34.783 0.00 0.00 0.00 2.41
158 165 7.880160 ATTTAAATCGAGGGAATTCACATGA 57.120 32.000 11.02 7.41 0.00 3.07
171 178 7.277098 GGGAATTCACATGATGATTTGTCTTTG 59.723 37.037 7.93 0.00 37.11 2.77
264 287 5.064962 ACATTTGCATTTTAATTCCATGCCG 59.935 36.000 11.80 3.80 42.31 5.69
297 320 3.023832 AGTTTCACCTCCAAACCTTGTG 58.976 45.455 0.00 0.00 34.76 3.33
301 324 3.909732 TCACCTCCAAACCTTGTGAATT 58.090 40.909 0.00 0.00 33.35 2.17
443 472 5.695816 TGCATTTGTGCCAACTTTCTATTTC 59.304 36.000 0.00 0.00 0.00 2.17
446 475 6.707440 TTTGTGCCAACTTTCTATTTCTCA 57.293 33.333 0.00 0.00 0.00 3.27
462 491 8.654094 TCTATTTCTCATGGATCAAGCTCATTA 58.346 33.333 0.00 0.00 0.00 1.90
475 504 2.432146 AGCTCATTATTGCGAGTCCAGA 59.568 45.455 0.00 0.00 0.00 3.86
522 552 9.557061 GTTTCTTCTCTAACCTTTTCCTTTCTA 57.443 33.333 0.00 0.00 0.00 2.10
600 639 0.413832 AACAGCCTCCCTCTCCACTA 59.586 55.000 0.00 0.00 0.00 2.74
602 641 0.260230 CAGCCTCCCTCTCCACTAGA 59.740 60.000 0.00 0.00 0.00 2.43
660 706 3.227276 CGACCCCCATCCTCTCGG 61.227 72.222 0.00 0.00 0.00 4.63
668 714 0.184933 CCATCCTCTCGGTCTCTCCT 59.815 60.000 0.00 0.00 0.00 3.69
691 737 1.152839 GTCTCCCTCTCCTCCCTCG 60.153 68.421 0.00 0.00 0.00 4.63
721 767 3.412722 GAGCCTCTCTCCTCGATCA 57.587 57.895 0.00 0.00 35.77 2.92
725 771 1.544724 CCTCTCTCCTCGATCATCCC 58.455 60.000 0.00 0.00 0.00 3.85
737 783 1.353694 GATCATCCCCTTCCCCTCATG 59.646 57.143 0.00 0.00 0.00 3.07
740 786 1.649271 ATCCCCTTCCCCTCATGTGC 61.649 60.000 0.00 0.00 0.00 4.57
743 789 2.046023 CTTCCCCTCATGTGCGCA 60.046 61.111 5.66 5.66 0.00 6.09
750 796 1.746239 CTCATGTGCGCATCCACCA 60.746 57.895 15.91 6.76 34.85 4.17
752 798 3.126879 ATGTGCGCATCCACCACG 61.127 61.111 15.91 0.00 34.85 4.94
764 810 1.376037 CACCACGCCCTTCCTTCTC 60.376 63.158 0.00 0.00 0.00 2.87
765 811 2.269241 CCACGCCCTTCCTTCTCC 59.731 66.667 0.00 0.00 0.00 3.71
766 812 2.269241 CACGCCCTTCCTTCTCCC 59.731 66.667 0.00 0.00 0.00 4.30
788 834 3.933722 CATCGCCATCGCCTCCCT 61.934 66.667 0.00 0.00 35.26 4.20
812 858 2.887568 CTGCGCCATCTGGTCGTC 60.888 66.667 4.18 7.33 37.17 4.20
813 859 3.362399 CTGCGCCATCTGGTCGTCT 62.362 63.158 4.18 0.00 37.17 4.18
816 862 1.226802 CGCCATCTGGTCGTCTGAG 60.227 63.158 0.00 0.00 37.57 3.35
840 886 3.443925 CTCCGCTCTGTCGCCTCA 61.444 66.667 0.00 0.00 0.00 3.86
845 891 2.575993 CTCTGTCGCCTCACCCTG 59.424 66.667 0.00 0.00 0.00 4.45
871 917 4.680237 CTCGTCGTGGCTGCCCAA 62.680 66.667 17.53 0.00 44.33 4.12
908 954 2.499685 CCTGTTCCCGGTCGGATC 59.500 66.667 11.39 1.78 41.63 3.36
952 998 4.767255 GCCAGGCCGTGTCCTCTG 62.767 72.222 0.00 0.00 33.25 3.35
964 1010 4.478371 CCTCTGCATCGCCAGCCA 62.478 66.667 0.00 0.00 32.87 4.75
976 1022 2.108976 CAGCCACCGATGCCGTAT 59.891 61.111 0.00 0.00 0.00 3.06
1017 1063 2.614969 ATGGCCCTGGCTTCCTCA 60.615 61.111 8.29 0.00 41.60 3.86
1020 1066 3.650950 GCCCTGGCTTCCTCACCA 61.651 66.667 0.00 0.00 38.26 4.17
1022 1068 1.077212 CCCTGGCTTCCTCACCATG 60.077 63.158 0.00 0.00 34.82 3.66
1024 1070 1.001764 CTGGCTTCCTCACCATGCA 60.002 57.895 0.00 0.00 34.82 3.96
1033 1079 0.320683 CTCACCATGCACGAACCTCA 60.321 55.000 0.00 0.00 0.00 3.86
1042 1088 3.864686 CGAACCTCAATGGCGCCG 61.865 66.667 23.90 7.87 40.22 6.46
1061 1107 2.818274 CGCCCTAAGGTTCGCCAC 60.818 66.667 0.00 0.00 40.60 5.01
1075 1121 4.530857 CCACCGGTCGCCTCATCC 62.531 72.222 2.59 0.00 0.00 3.51
1078 1124 3.917760 CCGGTCGCCTCATCCTCC 61.918 72.222 0.00 0.00 0.00 4.30
1084 1130 1.760086 CGCCTCATCCTCCAGGTCT 60.760 63.158 0.00 0.00 36.34 3.85
1086 1132 0.689080 GCCTCATCCTCCAGGTCTGA 60.689 60.000 0.00 0.00 36.34 3.27
1087 1133 1.118838 CCTCATCCTCCAGGTCTGAC 58.881 60.000 0.00 0.00 36.34 3.51
1088 1134 1.620798 CCTCATCCTCCAGGTCTGACA 60.621 57.143 10.38 0.00 36.34 3.58
1089 1135 2.182827 CTCATCCTCCAGGTCTGACAA 58.817 52.381 10.38 0.00 36.34 3.18
1090 1136 1.902508 TCATCCTCCAGGTCTGACAAC 59.097 52.381 10.38 0.00 36.34 3.32
1092 1138 0.469331 TCCTCCAGGTCTGACAACGT 60.469 55.000 10.38 0.00 36.34 3.99
1093 1139 0.038159 CCTCCAGGTCTGACAACGTC 60.038 60.000 10.38 0.00 0.00 4.34
1094 1140 0.038159 CTCCAGGTCTGACAACGTCC 60.038 60.000 10.38 0.00 0.00 4.79
1096 1142 0.038159 CCAGGTCTGACAACGTCCTC 60.038 60.000 10.38 0.00 0.00 3.71
1097 1143 0.387367 CAGGTCTGACAACGTCCTCG 60.387 60.000 10.38 0.00 43.34 4.63
1098 1144 1.080705 GGTCTGACAACGTCCTCGG 60.081 63.158 10.38 0.00 41.85 4.63
1099 1145 1.080705 GTCTGACAACGTCCTCGGG 60.081 63.158 2.24 0.00 41.85 5.14
1100 1146 1.228337 TCTGACAACGTCCTCGGGA 60.228 57.895 0.00 0.00 41.85 5.14
1101 1147 0.611062 TCTGACAACGTCCTCGGGAT 60.611 55.000 0.00 0.00 41.85 3.85
1102 1148 0.179134 CTGACAACGTCCTCGGGATC 60.179 60.000 0.00 0.00 41.85 3.36
1103 1149 1.141234 GACAACGTCCTCGGGATCC 59.859 63.158 1.92 1.92 41.85 3.36
1104 1150 1.601419 GACAACGTCCTCGGGATCCA 61.601 60.000 15.23 0.00 41.85 3.41
1105 1151 1.153628 CAACGTCCTCGGGATCCAC 60.154 63.158 15.23 1.14 41.85 4.02
1106 1152 2.707849 AACGTCCTCGGGATCCACG 61.708 63.158 15.23 16.48 41.85 4.94
1107 1153 3.138798 CGTCCTCGGGATCCACGT 61.139 66.667 15.23 0.00 32.73 4.49
1108 1154 2.806237 GTCCTCGGGATCCACGTC 59.194 66.667 15.23 0.00 32.73 4.34
1109 1155 2.827190 TCCTCGGGATCCACGTCG 60.827 66.667 15.23 7.99 0.00 5.12
1110 1156 3.900892 CCTCGGGATCCACGTCGG 61.901 72.222 15.23 14.48 0.00 4.79
1111 1157 3.138798 CTCGGGATCCACGTCGGT 61.139 66.667 15.23 0.00 35.57 4.69
1112 1158 3.411418 CTCGGGATCCACGTCGGTG 62.411 68.421 15.23 1.42 43.99 4.94
1113 1159 3.755628 CGGGATCCACGTCGGTGT 61.756 66.667 15.23 0.00 42.80 4.16
1114 1160 2.183555 GGGATCCACGTCGGTGTC 59.816 66.667 15.23 4.59 42.80 3.67
1121 1167 2.203451 ACGTCGGTGTCCAGTCCT 60.203 61.111 0.00 0.00 0.00 3.85
1185 1257 3.710722 CCCGAGTGCCTTCTGCCT 61.711 66.667 0.00 0.00 40.16 4.75
1190 1262 2.743928 GTGCCTTCTGCCTGTCCG 60.744 66.667 0.00 0.00 40.16 4.79
1193 1265 2.743928 CCTTCTGCCTGTCCGTGC 60.744 66.667 0.00 0.00 0.00 5.34
1210 1282 1.750399 GCCGCCATCCTGTTCATGT 60.750 57.895 0.00 0.00 0.00 3.21
1213 1285 1.167851 CGCCATCCTGTTCATGTTGT 58.832 50.000 0.00 0.00 0.00 3.32
1222 1294 1.270571 TGTTCATGTTGTAGCCTCGCA 60.271 47.619 0.00 0.00 0.00 5.10
1241 1314 2.731572 CATTGACTTCCCCTGCTCAAT 58.268 47.619 0.00 0.00 34.37 2.57
1244 1317 1.000396 ACTTCCCCTGCTCAATGGC 60.000 57.895 0.00 0.00 0.00 4.40
1246 1319 0.396695 CTTCCCCTGCTCAATGGCAT 60.397 55.000 0.00 0.00 41.63 4.40
1256 1329 2.141517 CTCAATGGCATCTCGTCATCC 58.858 52.381 0.00 0.00 39.71 3.51
1258 1331 0.109342 AATGGCATCTCGTCATCCCC 59.891 55.000 0.00 0.00 39.71 4.81
1261 1334 1.596477 GCATCTCGTCATCCCCAGC 60.596 63.158 0.00 0.00 0.00 4.85
1265 1338 4.147449 TCGTCATCCCCAGCGCTG 62.147 66.667 30.52 30.52 0.00 5.18
1288 1361 0.955428 TGCTCGAATCAAGTGCCACC 60.955 55.000 0.00 0.00 0.00 4.61
1294 1367 1.541588 GAATCAAGTGCCACCAAGTCC 59.458 52.381 0.00 0.00 0.00 3.85
1310 1383 1.487976 AGTCCCTGATGAATGCGACAT 59.512 47.619 0.00 0.00 0.00 3.06
1320 1393 2.482796 AATGCGACATGTCCCTGGCA 62.483 55.000 22.75 22.75 34.60 4.92
1325 1398 0.678048 GACATGTCCCTGGCAAGACC 60.678 60.000 15.31 0.00 39.84 3.85
1328 1401 4.410400 GTCCCTGGCAAGACCCGG 62.410 72.222 0.00 0.00 42.43 5.73
1334 1408 1.852067 CTGGCAAGACCCGGTTTTCG 61.852 60.000 0.00 0.00 37.83 3.46
1348 1422 3.121563 CGGTTTTCGTCAAGTTCGACTAC 60.122 47.826 0.00 0.00 37.05 2.73
1350 1424 3.338818 TTTCGTCAAGTTCGACTACGT 57.661 42.857 0.00 0.00 40.69 3.57
1360 1434 1.741528 TCGACTACGTGGCTATGACA 58.258 50.000 0.00 0.00 40.69 3.58
1371 1445 3.567164 GTGGCTATGACATCAGATTTGGG 59.433 47.826 0.00 0.00 0.00 4.12
1372 1446 2.555757 GGCTATGACATCAGATTTGGGC 59.444 50.000 0.00 0.00 0.00 5.36
1417 1491 1.141881 CGCCAAGGTCGACTATGCT 59.858 57.895 16.46 0.26 0.00 3.79
1418 1492 0.460284 CGCCAAGGTCGACTATGCTT 60.460 55.000 16.46 7.24 0.00 3.91
1419 1493 1.009829 GCCAAGGTCGACTATGCTTG 58.990 55.000 16.46 18.29 0.00 4.01
1421 1495 2.743183 GCCAAGGTCGACTATGCTTGAT 60.743 50.000 24.86 0.00 0.00 2.57
1424 1498 3.724508 AGGTCGACTATGCTTGATGAG 57.275 47.619 16.46 0.00 0.00 2.90
1426 1500 2.131183 GTCGACTATGCTTGATGAGGC 58.869 52.381 8.70 0.00 0.00 4.70
1441 1515 0.108756 GAGGCGACAAGTACCTCCAC 60.109 60.000 9.53 0.00 43.54 4.02
1465 1539 1.195448 TGACTCGAACGTCTACGAACC 59.805 52.381 9.86 8.20 43.02 3.62
1466 1540 1.195448 GACTCGAACGTCTACGAACCA 59.805 52.381 9.86 0.00 43.02 3.67
1510 1584 0.528901 CGTCGAGTGAACAACCACCA 60.529 55.000 0.00 0.00 37.76 4.17
1514 1588 1.782028 GAGTGAACAACCACCACCGC 61.782 60.000 0.00 0.00 37.76 5.68
1521 1595 2.742116 AACCACCACCGCTGTGAGT 61.742 57.895 10.15 3.37 45.76 3.41
1525 1599 2.338620 CCACCGCTGTGAGTTCGA 59.661 61.111 10.15 0.00 45.76 3.71
1554 1628 0.109597 GTGTGTACCACTACCGTCGG 60.110 60.000 10.48 10.48 41.11 4.79
1604 1678 0.179004 TCGCTGTGACCCCAAACATT 60.179 50.000 0.00 0.00 0.00 2.71
1605 1679 1.072489 TCGCTGTGACCCCAAACATTA 59.928 47.619 0.00 0.00 0.00 1.90
1627 1701 7.946918 TTAACGAAATGCGAATGACTATTTG 57.053 32.000 0.00 0.00 44.57 2.32
1637 1711 4.212004 CGAATGACTATTTGCCACGATGAT 59.788 41.667 0.00 0.00 0.00 2.45
1655 1743 2.555325 TGATCCGTGAACAACTACGACT 59.445 45.455 0.00 0.00 42.54 4.18
1665 1756 5.068198 TGAACAACTACGACTCTTTGTACCT 59.932 40.000 0.00 0.00 31.92 3.08
1668 1759 5.154932 CAACTACGACTCTTTGTACCTGAG 58.845 45.833 0.00 0.00 0.00 3.35
1669 1760 4.396522 ACTACGACTCTTTGTACCTGAGT 58.603 43.478 10.83 10.83 42.87 3.41
1710 1804 5.505780 TCAAAGGTATAACCACCAAGATGG 58.494 41.667 0.00 0.00 41.95 3.51
1743 1838 3.542097 CGAATGCATGTGTGTCGTATGAC 60.542 47.826 8.21 8.21 45.71 3.06
1781 1877 1.135024 GTGCCCGAATTGTCATTGCAT 60.135 47.619 0.00 0.00 0.00 3.96
1797 1893 1.202758 TGCATGTTCCTCCTCGTTTGT 60.203 47.619 0.00 0.00 0.00 2.83
1799 1895 1.726791 CATGTTCCTCCTCGTTTGTCG 59.273 52.381 0.00 0.00 41.41 4.35
1820 1917 2.571216 CCGTCGACCTGTGGGAACT 61.571 63.158 10.58 0.00 36.25 3.01
1847 1945 2.089982 ACCAGGATCATCCCACCATCTA 60.090 50.000 0.00 0.00 37.19 1.98
1922 2025 3.949132 TGTCGGATCATTGGAATGTTGA 58.051 40.909 0.00 0.00 37.65 3.18
1986 2091 1.102154 CCGCCATGGTGAAAATGCTA 58.898 50.000 27.12 0.00 0.00 3.49
1996 2101 6.832520 TGGTGAAAATGCTACATAACATGT 57.167 33.333 0.00 0.00 46.92 3.21
2141 2254 5.933463 ACCGGAATTGTCGTTTATTGTTCTA 59.067 36.000 9.46 0.00 0.00 2.10
2162 2275 6.113411 TCTAGCCTCATTTAAACTTGCCTAC 58.887 40.000 0.00 0.00 0.00 3.18
2266 2381 8.415950 ACTAAATAATTGGATGTGGTGTTTCA 57.584 30.769 0.00 0.00 0.00 2.69
2296 2411 4.240096 GCAACTTGTTGCATATTGAGCTT 58.760 39.130 27.19 0.00 46.60 3.74
2334 2451 7.721402 AGTATTGTTTGTTGCACTTTTCCATA 58.279 30.769 0.00 0.00 0.00 2.74
2341 2458 1.472082 TGCACTTTTCCATACCATGCG 59.528 47.619 0.00 0.00 34.32 4.73
2350 2467 3.599343 TCCATACCATGCGATGCTATTC 58.401 45.455 0.00 0.00 0.00 1.75
2356 2473 2.358582 CCATGCGATGCTATTCAAACCA 59.641 45.455 0.00 0.00 0.00 3.67
2459 2578 4.633565 GCTTCTCCTTGATAGTTCCAGTTG 59.366 45.833 0.00 0.00 0.00 3.16
2462 2581 1.398390 CCTTGATAGTTCCAGTTGCGC 59.602 52.381 0.00 0.00 0.00 6.09
2464 2583 2.472695 TGATAGTTCCAGTTGCGCTT 57.527 45.000 9.73 0.00 0.00 4.68
2466 2585 2.028112 TGATAGTTCCAGTTGCGCTTCT 60.028 45.455 9.73 3.76 0.00 2.85
2468 2587 1.230324 AGTTCCAGTTGCGCTTCTTC 58.770 50.000 9.73 0.00 0.00 2.87
2469 2588 1.202698 AGTTCCAGTTGCGCTTCTTCT 60.203 47.619 9.73 0.00 0.00 2.85
2471 2590 1.229428 TCCAGTTGCGCTTCTTCTTG 58.771 50.000 9.73 0.00 0.00 3.02
2477 2596 1.662517 TGCGCTTCTTCTTGTGTGAA 58.337 45.000 9.73 0.00 0.00 3.18
2512 2631 3.149196 ACGTTGGGTCGTCTACTTCTTA 58.851 45.455 0.00 0.00 40.04 2.10
2554 2673 3.359950 GGGATTTCAGGCAAGATGACTT 58.640 45.455 0.00 0.00 29.42 3.01
2576 2695 7.376615 ACTTTCACCTTGTATCACACTACTAC 58.623 38.462 0.00 0.00 0.00 2.73
2598 2718 4.020218 ACCTTTGCTATGCTAGTTGTCTCA 60.020 41.667 0.00 0.00 0.00 3.27
2604 2724 4.025061 GCTATGCTAGTTGTCTCAATGCTG 60.025 45.833 0.00 0.00 0.00 4.41
2625 2745 1.262417 TCGTTATGTCGCGCTACCTAG 59.738 52.381 9.82 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 5.878406 TTAAAAAGGGGTTGCAAGATGAA 57.122 34.783 0.00 0.00 0.00 2.57
158 165 9.125026 GGAGGATATGTTACAAAGACAAATCAT 57.875 33.333 0.00 0.00 0.00 2.45
171 178 9.462606 CCCTAAAATATTGGGAGGATATGTTAC 57.537 37.037 3.66 0.00 43.47 2.50
264 287 2.620585 AGGTGAAACTTGAAGCAGAAGC 59.379 45.455 0.00 0.00 37.92 3.86
319 344 4.762289 TGAGAATTTAGGAAGAGGCTCC 57.238 45.455 11.71 0.00 35.51 4.70
323 348 9.415544 CAAAAATGTTGAGAATTTAGGAAGAGG 57.584 33.333 0.00 0.00 0.00 3.69
425 452 5.183713 CCATGAGAAATAGAAAGTTGGCACA 59.816 40.000 0.00 0.00 0.00 4.57
443 472 5.617087 CGCAATAATGAGCTTGATCCATGAG 60.617 44.000 0.00 0.00 0.00 2.90
446 475 4.392047 TCGCAATAATGAGCTTGATCCAT 58.608 39.130 0.00 0.00 0.00 3.41
462 491 6.678900 GCAGATAATTTTTCTGGACTCGCAAT 60.679 38.462 15.68 0.00 40.77 3.56
475 504 7.662669 AGAAACTTTGGCATGCAGATAATTTTT 59.337 29.630 21.36 7.62 0.00 1.94
600 639 4.035102 GCTTTGGGAGGCCGGTCT 62.035 66.667 9.26 9.26 0.00 3.85
660 706 1.064979 AGGGAGACGAGAAGGAGAGAC 60.065 57.143 0.00 0.00 0.00 3.36
668 714 0.256464 GGAGGAGAGGGAGACGAGAA 59.744 60.000 0.00 0.00 0.00 2.87
711 757 0.972883 GGAAGGGGATGATCGAGGAG 59.027 60.000 0.00 0.00 0.00 3.69
721 767 1.649271 GCACATGAGGGGAAGGGGAT 61.649 60.000 0.00 0.00 0.00 3.85
725 771 2.825836 GCGCACATGAGGGGAAGG 60.826 66.667 0.30 0.00 0.00 3.46
743 789 2.198304 GAAGGAAGGGCGTGGTGGAT 62.198 60.000 0.00 0.00 0.00 3.41
750 796 3.009714 GGGGAGAAGGAAGGGCGT 61.010 66.667 0.00 0.00 0.00 5.68
772 818 3.620785 GAGGGAGGCGATGGCGAT 61.621 66.667 0.00 0.00 41.24 4.58
806 852 2.813042 GCAGCAGCTCAGACGACC 60.813 66.667 0.00 0.00 37.91 4.79
828 874 2.575993 CAGGGTGAGGCGACAGAG 59.424 66.667 0.00 0.00 0.00 3.35
845 891 4.436998 CACGACGAGGTCCCTGGC 62.437 72.222 0.00 0.00 0.00 4.85
943 989 1.812922 CTGGCGATGCAGAGGACAC 60.813 63.158 0.00 0.00 0.00 3.67
998 1044 3.728292 GAGGAAGCCAGGGCCATGG 62.728 68.421 32.24 32.24 43.17 3.66
1000 1046 2.614969 TGAGGAAGCCAGGGCCAT 60.615 61.111 6.18 0.00 43.17 4.40
1001 1047 3.650950 GTGAGGAAGCCAGGGCCA 61.651 66.667 6.18 0.00 43.17 5.36
1011 1057 0.605319 GGTTCGTGCATGGTGAGGAA 60.605 55.000 5.98 0.00 0.00 3.36
1017 1063 1.167851 CATTGAGGTTCGTGCATGGT 58.832 50.000 5.98 0.00 0.00 3.55
1020 1066 1.647545 CGCCATTGAGGTTCGTGCAT 61.648 55.000 0.00 0.00 40.61 3.96
1022 1068 2.480555 CGCCATTGAGGTTCGTGC 59.519 61.111 0.00 0.00 40.61 5.34
1024 1070 2.746277 GGCGCCATTGAGGTTCGT 60.746 61.111 24.80 0.00 40.61 3.85
1061 1107 3.917760 GGAGGATGAGGCGACCGG 61.918 72.222 0.00 0.00 0.00 5.28
1074 1120 0.038159 GACGTTGTCAGACCTGGAGG 60.038 60.000 0.00 0.00 35.30 4.30
1075 1121 0.038159 GGACGTTGTCAGACCTGGAG 60.038 60.000 0.00 0.00 33.68 3.86
1078 1124 0.387367 CGAGGACGTTGTCAGACCTG 60.387 60.000 0.00 0.00 34.14 4.00
1084 1130 1.601419 GGATCCCGAGGACGTTGTCA 61.601 60.000 0.00 0.00 32.98 3.58
1086 1132 1.608336 TGGATCCCGAGGACGTTGT 60.608 57.895 9.90 0.00 32.98 3.32
1087 1133 1.153628 GTGGATCCCGAGGACGTTG 60.154 63.158 9.90 0.00 32.98 4.10
1088 1134 2.707849 CGTGGATCCCGAGGACGTT 61.708 63.158 9.90 0.00 32.98 3.99
1089 1135 3.138798 CGTGGATCCCGAGGACGT 61.139 66.667 9.90 0.00 32.98 4.34
1090 1136 3.122250 GACGTGGATCCCGAGGACG 62.122 68.421 23.89 20.73 32.98 4.79
1092 1138 2.827190 CGACGTGGATCCCGAGGA 60.827 66.667 23.89 0.00 35.55 3.71
1093 1139 3.900892 CCGACGTGGATCCCGAGG 61.901 72.222 23.89 20.85 42.00 4.63
1094 1140 3.138798 ACCGACGTGGATCCCGAG 61.139 66.667 23.89 17.32 42.00 4.63
1096 1142 3.695022 GACACCGACGTGGATCCCG 62.695 68.421 17.75 17.75 44.86 5.14
1097 1143 2.183555 GACACCGACGTGGATCCC 59.816 66.667 9.90 0.00 44.86 3.85
1098 1144 2.183555 GGACACCGACGTGGATCC 59.816 66.667 4.20 4.20 44.86 3.36
1099 1145 1.153823 CTGGACACCGACGTGGATC 60.154 63.158 10.46 7.46 44.86 3.36
1100 1146 1.874345 GACTGGACACCGACGTGGAT 61.874 60.000 10.46 0.00 44.86 3.41
1101 1147 2.520020 ACTGGACACCGACGTGGA 60.520 61.111 10.46 0.00 44.86 4.02
1102 1148 2.049433 GACTGGACACCGACGTGG 60.049 66.667 0.00 0.00 44.86 4.94
1103 1149 2.049433 GGACTGGACACCGACGTG 60.049 66.667 0.00 0.00 46.11 4.49
1104 1150 2.203451 AGGACTGGACACCGACGT 60.203 61.111 0.00 0.00 0.00 4.34
1105 1151 2.258591 CAGGACTGGACACCGACG 59.741 66.667 0.00 0.00 0.00 5.12
1106 1152 1.289380 GACAGGACTGGACACCGAC 59.711 63.158 4.14 0.00 34.19 4.79
1107 1153 1.906824 GGACAGGACTGGACACCGA 60.907 63.158 4.14 0.00 34.19 4.69
1108 1154 2.657237 GGACAGGACTGGACACCG 59.343 66.667 4.14 0.00 34.19 4.94
1109 1155 2.593956 GGGGACAGGACTGGACACC 61.594 68.421 4.14 4.52 34.19 4.16
1110 1156 2.943978 CGGGGACAGGACTGGACAC 61.944 68.421 4.14 0.00 34.19 3.67
1111 1157 2.603473 CGGGGACAGGACTGGACA 60.603 66.667 4.14 0.00 34.19 4.02
1112 1158 2.283676 TCGGGGACAGGACTGGAC 60.284 66.667 4.14 0.00 34.19 4.02
1113 1159 2.283676 GTCGGGGACAGGACTGGA 60.284 66.667 4.14 0.00 31.92 3.86
1114 1160 3.391382 GGTCGGGGACAGGACTGG 61.391 72.222 4.14 0.00 34.46 4.00
1161 1233 1.183549 GAAGGCACTCGGGTTAGAGA 58.816 55.000 0.62 0.00 38.49 3.10
1165 1237 1.295423 GCAGAAGGCACTCGGGTTA 59.705 57.895 0.00 0.00 38.49 2.85
1190 1262 1.750399 ATGAACAGGATGGCGGCAC 60.750 57.895 16.34 8.50 43.62 5.01
1193 1265 0.452987 CAACATGAACAGGATGGCGG 59.547 55.000 0.00 0.00 43.62 6.13
1196 1268 2.684881 GGCTACAACATGAACAGGATGG 59.315 50.000 0.00 0.00 43.62 3.51
1198 1270 3.679917 CGAGGCTACAACATGAACAGGAT 60.680 47.826 0.00 0.00 0.00 3.24
1210 1282 2.346803 GAAGTCAATGCGAGGCTACAA 58.653 47.619 0.00 0.00 0.00 2.41
1213 1285 0.178068 GGGAAGTCAATGCGAGGCTA 59.822 55.000 0.00 0.00 0.00 3.93
1222 1294 2.622452 CCATTGAGCAGGGGAAGTCAAT 60.622 50.000 0.00 0.00 39.65 2.57
1241 1314 1.688884 TGGGGATGACGAGATGCCA 60.689 57.895 10.20 0.00 35.56 4.92
1244 1317 1.300465 CGCTGGGGATGACGAGATG 60.300 63.158 0.00 0.00 0.00 2.90
1246 1319 3.838271 GCGCTGGGGATGACGAGA 61.838 66.667 0.00 0.00 0.00 4.04
1261 1334 3.267860 GATTCGAGCAGGGCAGCG 61.268 66.667 0.00 0.00 40.15 5.18
1265 1338 1.986575 GCACTTGATTCGAGCAGGGC 61.987 60.000 0.49 0.25 0.00 5.19
1270 1343 0.955428 TGGTGGCACTTGATTCGAGC 60.955 55.000 18.45 0.00 0.00 5.03
1272 1345 1.202758 ACTTGGTGGCACTTGATTCGA 60.203 47.619 18.45 0.00 0.00 3.71
1276 1349 0.251341 GGGACTTGGTGGCACTTGAT 60.251 55.000 18.45 0.91 0.00 2.57
1288 1361 1.667724 GTCGCATTCATCAGGGACTTG 59.332 52.381 0.00 0.00 42.40 3.16
1294 1367 1.600957 GGACATGTCGCATTCATCAGG 59.399 52.381 19.33 0.00 0.00 3.86
1310 1383 3.636231 CGGGTCTTGCCAGGGACA 61.636 66.667 0.00 0.00 39.65 4.02
1320 1393 1.134310 ACTTGACGAAAACCGGGTCTT 60.134 47.619 6.32 0.00 43.93 3.01
1325 1398 1.071041 GTCGAACTTGACGAAAACCGG 60.071 52.381 0.00 0.00 43.93 5.28
1328 1401 3.483558 ACGTAGTCGAACTTGACGAAAAC 59.516 43.478 13.50 0.00 43.70 2.43
1334 1408 1.058404 GCCACGTAGTCGAACTTGAC 58.942 55.000 0.00 0.00 41.61 3.18
1348 1422 3.249320 CCAAATCTGATGTCATAGCCACG 59.751 47.826 0.00 0.00 0.00 4.94
1350 1424 3.824133 CCCAAATCTGATGTCATAGCCA 58.176 45.455 0.00 0.00 0.00 4.75
1360 1434 1.669999 GCTTGCGGCCCAAATCTGAT 61.670 55.000 0.00 0.00 31.94 2.90
1371 1445 2.561373 GTACTTGGTGCTTGCGGC 59.439 61.111 0.00 0.00 42.22 6.53
1372 1446 2.332654 GGGTACTTGGTGCTTGCGG 61.333 63.158 0.00 0.00 0.00 5.69
1417 1491 1.899814 AGGTACTTGTCGCCTCATCAA 59.100 47.619 0.00 0.00 27.25 2.57
1418 1492 1.476891 GAGGTACTTGTCGCCTCATCA 59.523 52.381 14.88 0.00 45.93 3.07
1419 1493 2.211353 GAGGTACTTGTCGCCTCATC 57.789 55.000 14.88 0.00 45.93 2.92
1424 1498 1.079336 GGTGGAGGTACTTGTCGCC 60.079 63.158 0.00 0.00 41.55 5.54
1426 1500 0.815734 ATCGGTGGAGGTACTTGTCG 59.184 55.000 0.00 0.00 41.55 4.35
1441 1515 1.591632 CGTAGACGTTCGAGTCATCGG 60.592 57.143 7.47 0.00 43.24 4.18
1485 1559 0.179067 TTGTTCACTCGACGGCCTTT 60.179 50.000 0.00 0.00 0.00 3.11
1492 1566 0.935196 GTGGTGGTTGTTCACTCGAC 59.065 55.000 0.00 0.00 37.75 4.20
1498 1572 1.821759 CAGCGGTGGTGGTTGTTCA 60.822 57.895 6.74 0.00 0.00 3.18
1510 1584 0.597637 CTTGTCGAACTCACAGCGGT 60.598 55.000 0.00 0.00 0.00 5.68
1514 1588 3.306166 ACGTTTTCTTGTCGAACTCACAG 59.694 43.478 0.00 0.00 0.00 3.66
1521 1595 3.306703 GGTACACACGTTTTCTTGTCGAA 59.693 43.478 0.00 0.00 29.73 3.71
1554 1628 1.446272 CCACGGAGTCTTCGAAGGC 60.446 63.158 22.08 22.08 41.61 4.35
1604 1678 5.963004 GCAAATAGTCATTCGCATTTCGTTA 59.037 36.000 0.00 0.00 39.67 3.18
1605 1679 4.793216 GCAAATAGTCATTCGCATTTCGTT 59.207 37.500 0.00 0.00 39.67 3.85
1614 1688 3.555547 TCATCGTGGCAAATAGTCATTCG 59.444 43.478 0.00 0.00 32.25 3.34
1618 1692 3.466836 GGATCATCGTGGCAAATAGTCA 58.533 45.455 0.00 0.00 0.00 3.41
1637 1711 2.224606 AGAGTCGTAGTTGTTCACGGA 58.775 47.619 0.00 0.00 38.66 4.69
1655 1743 2.872732 AGGACGACTCAGGTACAAAGA 58.127 47.619 0.00 0.00 0.00 2.52
1710 1804 1.315257 ATGCATTCGTCCAAGGGTGC 61.315 55.000 0.00 0.00 0.00 5.01
1781 1877 0.748450 ACGACAAACGAGGAGGAACA 59.252 50.000 0.00 0.00 45.77 3.18
1811 1908 1.553248 CCTGGTTATCGAGTTCCCACA 59.447 52.381 0.00 0.00 0.00 4.17
1820 1917 2.632996 GTGGGATGATCCTGGTTATCGA 59.367 50.000 11.87 0.00 36.57 3.59
1922 2025 0.602562 CAATGGAAATGGTGCCACGT 59.397 50.000 0.00 0.00 36.92 4.49
2023 2129 9.869844 GATGCAGATGACATATACAAGTTTTAC 57.130 33.333 0.00 0.00 0.00 2.01
2097 2204 5.373222 CGGTAAATCCCCATGTCATTTAGA 58.627 41.667 0.00 0.00 0.00 2.10
2141 2254 4.662278 TGTAGGCAAGTTTAAATGAGGCT 58.338 39.130 14.12 14.12 35.91 4.58
2162 2275 9.561069 AGGTGAAGCATAATAAAACTACCTATG 57.439 33.333 0.00 0.00 33.38 2.23
2233 2347 8.960591 CCACATCCAATTATTTAGTTCACTCTT 58.039 33.333 0.00 0.00 0.00 2.85
2334 2451 2.358898 GGTTTGAATAGCATCGCATGGT 59.641 45.455 0.00 6.19 44.27 3.55
2341 2458 4.096833 TGCATGTCTGGTTTGAATAGCATC 59.903 41.667 0.00 0.00 0.00 3.91
2350 2467 4.456911 ACAAGTAGATGCATGTCTGGTTTG 59.543 41.667 2.46 6.37 0.00 2.93
2356 2473 4.083110 GCACAAACAAGTAGATGCATGTCT 60.083 41.667 2.46 0.00 33.27 3.41
2459 2578 2.306799 CTTCACACAAGAAGAAGCGC 57.693 50.000 0.00 0.00 46.18 5.92
2466 2585 4.690748 GTCGAATGGATCTTCACACAAGAA 59.309 41.667 0.00 0.00 0.00 2.52
2468 2587 4.248859 AGTCGAATGGATCTTCACACAAG 58.751 43.478 0.00 0.00 0.00 3.16
2469 2588 4.271696 AGTCGAATGGATCTTCACACAA 57.728 40.909 0.00 0.00 0.00 3.33
2471 2590 3.791887 CGTAGTCGAATGGATCTTCACAC 59.208 47.826 0.00 0.00 39.71 3.82
2477 2596 2.100916 CCCAACGTAGTCGAATGGATCT 59.899 50.000 14.56 0.00 45.00 2.75
2512 2631 3.254657 CCGCTAGGAAGAAGATCGAATCT 59.745 47.826 0.00 0.00 39.98 2.40
2554 2673 6.014647 AGGTAGTAGTGTGATACAAGGTGAA 58.985 40.000 0.00 0.00 0.00 3.18
2563 2682 6.323996 AGCATAGCAAAGGTAGTAGTGTGATA 59.676 38.462 0.00 0.00 0.00 2.15
2576 2695 4.507710 TGAGACAACTAGCATAGCAAAGG 58.492 43.478 0.00 0.00 44.39 3.11
2598 2718 0.645355 CGCGACATAACGACAGCATT 59.355 50.000 0.00 0.00 35.09 3.56
2604 2724 0.248377 AGGTAGCGCGACATAACGAC 60.248 55.000 22.25 2.95 35.09 4.34


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

AutoCloner maintained by Alex Coulton.