Multiple sequence alignment - TraesCS3D01G288500

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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 TraesCS3D01G288500 chr3D 100.000 2523 0 0 1 2523 397200552 397203074 0.000000e+00 4660.0
1 TraesCS3D01G288500 chr3D 98.750 880 11 0 1644 2523 84493330 84492451 0.000000e+00 1565.0
2 TraesCS3D01G288500 chr3D 87.023 655 61 13 1625 2278 92361350 92361981 0.000000e+00 717.0
3 TraesCS3D01G288500 chr3D 77.228 606 71 30 17 595 397208278 397208843 2.450000e-75 292.0
4 TraesCS3D01G288500 chr7D 99.114 903 8 0 1621 2523 273666143 273667045 0.000000e+00 1624.0
5 TraesCS3D01G288500 chr7D 98.998 898 8 1 1626 2523 182511519 182510623 0.000000e+00 1607.0
6 TraesCS3D01G288500 chr7D 81.741 586 58 19 155 711 561620312 561620877 6.400000e-121 444.0
7 TraesCS3D01G288500 chr2D 97.795 907 10 4 1625 2523 53958719 53959623 0.000000e+00 1555.0
8 TraesCS3D01G288500 chr2D 87.934 547 50 6 1625 2157 16061767 16062311 4.580000e-177 630.0
9 TraesCS3D01G288500 chr2D 90.237 338 32 1 2187 2523 16062308 16062645 8.280000e-120 440.0
10 TraesCS3D01G288500 chr3B 87.341 1098 83 22 1 1065 523147171 523148245 0.000000e+00 1206.0
11 TraesCS3D01G288500 chr3B 85.011 467 50 9 1628 2093 542721485 542721038 8.230000e-125 457.0
12 TraesCS3D01G288500 chr3B 87.121 396 30 13 1200 1595 523148389 523148763 1.790000e-116 429.0
13 TraesCS3D01G288500 chr3B 78.170 623 71 36 30 624 523150939 523151524 1.120000e-88 337.0
14 TraesCS3D01G288500 chr3B 100.000 43 0 0 672 714 523151529 523151571 2.080000e-11 80.5
15 TraesCS3D01G288500 chr7A 90.749 908 52 17 1625 2523 663818721 663817837 0.000000e+00 1182.0
16 TraesCS3D01G288500 chr7A 92.553 564 38 2 1961 2523 663820647 663820087 0.000000e+00 806.0
17 TraesCS3D01G288500 chr7A 88.859 368 38 3 1707 2073 431260307 431259942 1.380000e-122 449.0
18 TraesCS3D01G288500 chr3A 88.812 867 65 16 2 849 516789100 516789953 0.000000e+00 1035.0
19 TraesCS3D01G288500 chr3A 80.184 762 97 28 853 1596 516790069 516790794 2.880000e-144 521.0
20 TraesCS3D01G288500 chr3A 84.980 506 26 24 160 653 516792981 516793448 3.800000e-128 468.0
21 TraesCS3D01G288500 chr3A 85.976 164 11 4 436 595 516801121 516801276 5.580000e-37 165.0
22 TraesCS3D01G288500 chr3A 100.000 34 0 0 1593 1626 423255147 423255114 2.100000e-06 63.9
23 TraesCS3D01G288500 chr3A 100.000 34 0 0 1593 1626 423255276 423255243 2.100000e-06 63.9
24 TraesCS3D01G288500 chr6B 86.834 919 61 28 1624 2523 389254369 389253492 0.000000e+00 972.0
25 TraesCS3D01G288500 chr2A 94.291 578 29 4 1947 2523 25376920 25376346 0.000000e+00 881.0
26 TraesCS3D01G288500 chr2A 83.298 473 57 15 1625 2096 307074556 307075007 1.400000e-112 416.0
27 TraesCS3D01G288500 chr2A 92.727 110 6 1 1624 1733 25377458 25377351 9.340000e-35 158.0
28 TraesCS3D01G288500 chr5B 85.038 655 71 18 1625 2278 679009150 679009778 2.120000e-180 641.0
29 TraesCS3D01G288500 chr5B 86.492 533 40 15 1992 2523 330620398 330620899 7.880000e-155 556.0
30 TraesCS3D01G288500 chr5B 91.489 47 3 1 1584 1630 509463918 509463963 2.100000e-06 63.9
31 TraesCS3D01G288500 chr5B 100.000 34 0 0 1593 1626 686445178 686445145 2.100000e-06 63.9
32 TraesCS3D01G288500 chr7B 78.833 737 88 37 15 714 610347401 610348106 3.850000e-118 435.0
33 TraesCS3D01G288500 chr4D 82.625 259 27 15 1864 2110 24699943 24699691 1.970000e-51 213.0
34 TraesCS3D01G288500 chr4D 100.000 34 0 0 1593 1626 492941932 492941965 2.100000e-06 63.9
35 TraesCS3D01G288500 chr1B 100.000 36 0 0 1591 1626 631954302 631954267 1.620000e-07 67.6
36 TraesCS3D01G288500 chr5D 95.238 42 1 1 1593 1634 491656435 491656475 5.830000e-07 65.8
37 TraesCS3D01G288500 chr5A 100.000 35 0 0 1592 1626 689419168 689419202 5.830000e-07 65.8
38 TraesCS3D01G288500 chr4B 100.000 34 0 0 1593 1626 332564785 332564752 2.100000e-06 63.9


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 TraesCS3D01G288500 chr3D 397200552 397203074 2522 False 4660.000000 4660 100.000000 1 2523 1 chr3D.!!$F2 2522
1 TraesCS3D01G288500 chr3D 84492451 84493330 879 True 1565.000000 1565 98.750000 1644 2523 1 chr3D.!!$R1 879
2 TraesCS3D01G288500 chr3D 92361350 92361981 631 False 717.000000 717 87.023000 1625 2278 1 chr3D.!!$F1 653
3 TraesCS3D01G288500 chr3D 397208278 397208843 565 False 292.000000 292 77.228000 17 595 1 chr3D.!!$F3 578
4 TraesCS3D01G288500 chr7D 273666143 273667045 902 False 1624.000000 1624 99.114000 1621 2523 1 chr7D.!!$F1 902
5 TraesCS3D01G288500 chr7D 182510623 182511519 896 True 1607.000000 1607 98.998000 1626 2523 1 chr7D.!!$R1 897
6 TraesCS3D01G288500 chr7D 561620312 561620877 565 False 444.000000 444 81.741000 155 711 1 chr7D.!!$F2 556
7 TraesCS3D01G288500 chr2D 53958719 53959623 904 False 1555.000000 1555 97.795000 1625 2523 1 chr2D.!!$F1 898
8 TraesCS3D01G288500 chr2D 16061767 16062645 878 False 535.000000 630 89.085500 1625 2523 2 chr2D.!!$F2 898
9 TraesCS3D01G288500 chr3B 523147171 523151571 4400 False 513.125000 1206 88.158000 1 1595 4 chr3B.!!$F1 1594
10 TraesCS3D01G288500 chr7A 663817837 663820647 2810 True 994.000000 1182 91.651000 1625 2523 2 chr7A.!!$R2 898
11 TraesCS3D01G288500 chr3A 516789100 516793448 4348 False 674.666667 1035 84.658667 2 1596 3 chr3A.!!$F2 1594
12 TraesCS3D01G288500 chr6B 389253492 389254369 877 True 972.000000 972 86.834000 1624 2523 1 chr6B.!!$R1 899
13 TraesCS3D01G288500 chr2A 25376346 25377458 1112 True 519.500000 881 93.509000 1624 2523 2 chr2A.!!$R1 899
14 TraesCS3D01G288500 chr5B 679009150 679009778 628 False 641.000000 641 85.038000 1625 2278 1 chr5B.!!$F3 653
15 TraesCS3D01G288500 chr5B 330620398 330620899 501 False 556.000000 556 86.492000 1992 2523 1 chr5B.!!$F1 531
16 TraesCS3D01G288500 chr7B 610347401 610348106 705 False 435.000000 435 78.833000 15 714 1 chr7B.!!$F1 699

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
233 253 0.250295 CCACTCGGCCAAGACAAAGA 60.250 55.0 2.24 0.0 0.0 2.52 F
1055 1260 0.392336 ATGCTGATCTCCTTCCTCGC 59.608 55.0 0.00 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1110 1315 0.030638 GCCATTGTTTCGTGCACACT 59.969 50.0 18.64 0.0 0.0 3.55 R
1903 3366 0.695803 AGGGGAGAGCTATGGTTGGG 60.696 60.0 0.00 0.0 0.0 4.12 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
51 56 6.583806 CGATTTTCTGGTTGAAGAAATTCAGG 59.416 38.462 15.95 3.89 43.75 3.86
62 67 6.940739 TGAAGAAATTCAGGAAACACCAAAA 58.059 32.000 0.00 0.00 42.04 2.44
81 86 5.982516 CCAAAAGTCAATCAAAACCGATTCA 59.017 36.000 0.00 0.00 33.27 2.57
100 106 2.415168 TCATCGCGCGAAAAAGAAGAAT 59.585 40.909 38.07 13.56 0.00 2.40
130 136 0.394938 TTCCGGCTGCAGTAACTTGA 59.605 50.000 16.64 1.17 0.00 3.02
174 190 3.065371 ACGAAAAAGAAGACCTTGCACAG 59.935 43.478 0.00 0.00 34.79 3.66
185 201 2.486472 CTTGCACAGGAGATGGTCTT 57.514 50.000 0.00 0.00 0.00 3.01
231 251 0.817634 CACCACTCGGCCAAGACAAA 60.818 55.000 2.24 0.00 34.57 2.83
232 252 0.535102 ACCACTCGGCCAAGACAAAG 60.535 55.000 2.24 0.00 34.57 2.77
233 253 0.250295 CCACTCGGCCAAGACAAAGA 60.250 55.000 2.24 0.00 0.00 2.52
401 448 4.994852 TGAAACCGGAAATCTCTTGTACTG 59.005 41.667 9.46 0.00 0.00 2.74
406 453 3.585862 GGAAATCTCTTGTACTGACGCA 58.414 45.455 0.00 0.00 0.00 5.24
609 677 1.129251 CTTCATGCGTTCGCTTGTGAT 59.871 47.619 24.30 6.96 37.49 3.06
610 678 0.443478 TCATGCGTTCGCTTGTGATG 59.557 50.000 24.30 16.37 37.49 3.07
655 724 3.467803 GCGGTGCCAAATCTAGTAATCT 58.532 45.455 0.00 0.00 0.00 2.40
735 808 3.190535 CGTGCTAACAAGTAAAAGGGCAT 59.809 43.478 0.00 0.00 0.00 4.40
736 809 4.671766 CGTGCTAACAAGTAAAAGGGCATC 60.672 45.833 0.00 0.00 0.00 3.91
737 810 3.438781 TGCTAACAAGTAAAAGGGCATCG 59.561 43.478 0.00 0.00 0.00 3.84
739 812 4.155280 GCTAACAAGTAAAAGGGCATCGAA 59.845 41.667 0.00 0.00 0.00 3.71
757 830 6.403636 GCATCGAATCCAACTTGAACACTAAT 60.404 38.462 0.00 0.00 0.00 1.73
758 831 6.721571 TCGAATCCAACTTGAACACTAATC 57.278 37.500 0.00 0.00 0.00 1.75
759 832 5.642063 TCGAATCCAACTTGAACACTAATCC 59.358 40.000 0.00 0.00 0.00 3.01
762 835 4.072131 TCCAACTTGAACACTAATCCTGC 58.928 43.478 0.00 0.00 0.00 4.85
765 838 5.647658 CCAACTTGAACACTAATCCTGCATA 59.352 40.000 0.00 0.00 0.00 3.14
766 839 6.319658 CCAACTTGAACACTAATCCTGCATAT 59.680 38.462 0.00 0.00 0.00 1.78
767 840 7.498900 CCAACTTGAACACTAATCCTGCATATA 59.501 37.037 0.00 0.00 0.00 0.86
768 841 9.060347 CAACTTGAACACTAATCCTGCATATAT 57.940 33.333 0.00 0.00 0.00 0.86
769 842 8.839310 ACTTGAACACTAATCCTGCATATATC 57.161 34.615 0.00 0.00 0.00 1.63
779 868 4.436332 TCCTGCATATATCATAGCAAGCG 58.564 43.478 0.00 0.00 36.44 4.68
799 888 2.148768 GGTAACAAAGCTAGTGCGGTT 58.851 47.619 0.00 0.00 45.42 4.44
817 906 3.646976 CATCGCTGCCATCTGCCG 61.647 66.667 0.00 0.00 40.16 5.69
863 1064 1.089112 TCGATCAGTCCGCGAAACTA 58.911 50.000 8.23 0.85 0.00 2.24
883 1084 2.741985 TGGATGAACAGTGCGGCG 60.742 61.111 0.51 0.51 0.00 6.46
884 1085 4.166011 GGATGAACAGTGCGGCGC 62.166 66.667 27.44 27.44 0.00 6.53
932 1137 0.676782 GCACACCCCTACACATCCAC 60.677 60.000 0.00 0.00 0.00 4.02
934 1139 0.690762 ACACCCCTACACATCCACAC 59.309 55.000 0.00 0.00 0.00 3.82
941 1146 0.474854 TACACATCCACACCCCCACT 60.475 55.000 0.00 0.00 0.00 4.00
942 1147 1.303561 CACATCCACACCCCCACTG 60.304 63.158 0.00 0.00 0.00 3.66
963 1168 1.906574 CCTACCAGTAGCACTTTCCCA 59.093 52.381 0.00 0.00 31.95 4.37
964 1169 2.093447 CCTACCAGTAGCACTTTCCCAG 60.093 54.545 0.00 0.00 31.95 4.45
965 1170 1.435256 ACCAGTAGCACTTTCCCAGT 58.565 50.000 0.00 0.00 35.35 4.00
966 1171 1.774856 ACCAGTAGCACTTTCCCAGTT 59.225 47.619 0.00 0.00 30.92 3.16
967 1172 2.224548 ACCAGTAGCACTTTCCCAGTTC 60.225 50.000 0.00 0.00 30.92 3.01
968 1173 2.427506 CAGTAGCACTTTCCCAGTTCC 58.572 52.381 0.00 0.00 30.92 3.62
969 1174 2.054799 AGTAGCACTTTCCCAGTTCCA 58.945 47.619 0.00 0.00 30.92 3.53
978 1183 1.048601 TCCCAGTTCCAGTGTGACTC 58.951 55.000 0.00 0.00 0.00 3.36
987 1192 2.872001 GTGTGACTCGCGAGCTCG 60.872 66.667 34.83 31.37 43.27 5.03
988 1193 3.047877 TGTGACTCGCGAGCTCGA 61.048 61.111 38.74 18.68 43.02 4.04
989 1194 2.574736 GTGACTCGCGAGCTCGAC 60.575 66.667 38.74 26.70 43.02 4.20
990 1195 3.800863 TGACTCGCGAGCTCGACC 61.801 66.667 38.74 21.04 43.02 4.79
1055 1260 0.392336 ATGCTGATCTCCTTCCTCGC 59.608 55.000 0.00 0.00 0.00 5.03
1065 1270 4.689549 TTCCTCGCGGTCCAGGGA 62.690 66.667 6.13 0.00 0.00 4.20
1075 1280 4.974438 TCCAGGGAACGCTGGGGT 62.974 66.667 28.58 0.00 43.73 4.95
1076 1281 4.410400 CCAGGGAACGCTGGGGTC 62.410 72.222 24.08 0.39 41.17 4.46
1077 1282 4.410400 CAGGGAACGCTGGGGTCC 62.410 72.222 19.71 19.71 0.00 4.46
1080 1285 3.782443 GGAACGCTGGGGTCCGAT 61.782 66.667 13.39 0.00 0.00 4.18
1081 1286 2.267961 GAACGCTGGGGTCCGATT 59.732 61.111 0.00 0.00 0.00 3.34
1082 1287 1.376812 GAACGCTGGGGTCCGATTT 60.377 57.895 0.00 0.00 0.00 2.17
1083 1288 1.366854 GAACGCTGGGGTCCGATTTC 61.367 60.000 0.00 0.00 0.00 2.17
1086 1291 2.513897 CTGGGGTCCGATTTCGCC 60.514 66.667 0.00 0.00 38.18 5.54
1087 1292 4.460683 TGGGGTCCGATTTCGCCG 62.461 66.667 0.00 0.00 39.12 6.46
1105 1310 2.030412 CGTGCTACTGCCACCACA 59.970 61.111 0.00 0.00 38.71 4.17
1110 1315 1.028905 GCTACTGCCACCACAACAAA 58.971 50.000 0.00 0.00 0.00 2.83
1111 1316 1.001378 GCTACTGCCACCACAACAAAG 60.001 52.381 0.00 0.00 0.00 2.77
1112 1317 2.297701 CTACTGCCACCACAACAAAGT 58.702 47.619 0.00 0.00 0.00 2.66
1117 1322 0.529833 CCACCACAACAAAGTGTGCA 59.470 50.000 0.00 0.00 46.24 4.57
1118 1323 1.627879 CACCACAACAAAGTGTGCAC 58.372 50.000 10.75 10.75 46.24 4.57
1119 1324 0.170116 ACCACAACAAAGTGTGCACG 59.830 50.000 13.13 0.00 46.24 5.34
1122 1327 2.590073 CACAACAAAGTGTGCACGAAA 58.410 42.857 13.13 0.00 42.26 3.46
1123 1328 2.341168 CACAACAAAGTGTGCACGAAAC 59.659 45.455 13.13 4.91 42.26 2.78
1124 1329 2.030717 ACAACAAAGTGTGCACGAAACA 60.031 40.909 13.13 0.00 36.20 2.83
1125 1330 2.983136 CAACAAAGTGTGCACGAAACAA 59.017 40.909 13.13 0.00 36.20 2.83
1126 1331 3.502191 ACAAAGTGTGCACGAAACAAT 57.498 38.095 13.13 0.00 36.20 2.71
1135 1346 2.190170 ACGAAACAATGGCCACGCA 61.190 52.632 8.16 0.00 0.00 5.24
1153 1364 0.673333 CAAGCCGGTGTACTGCATGA 60.673 55.000 1.90 0.00 0.00 3.07
1165 1376 1.808945 ACTGCATGAAGAAAAGCCTCG 59.191 47.619 8.02 0.00 0.00 4.63
1167 1378 2.485426 CTGCATGAAGAAAAGCCTCGAA 59.515 45.455 0.00 0.00 0.00 3.71
1168 1379 2.485426 TGCATGAAGAAAAGCCTCGAAG 59.515 45.455 0.00 0.00 0.00 3.79
1170 1381 3.425492 GCATGAAGAAAAGCCTCGAAGAC 60.425 47.826 0.00 0.00 0.00 3.01
1174 1385 4.038763 TGAAGAAAAGCCTCGAAGACTGTA 59.961 41.667 0.00 0.00 0.00 2.74
1175 1386 3.915536 AGAAAAGCCTCGAAGACTGTAC 58.084 45.455 0.00 0.00 0.00 2.90
1177 1388 0.526662 AAGCCTCGAAGACTGTACCG 59.473 55.000 0.00 0.00 0.00 4.02
1178 1389 1.139095 GCCTCGAAGACTGTACCGG 59.861 63.158 0.00 0.00 0.00 5.28
1179 1390 1.139095 CCTCGAAGACTGTACCGGC 59.861 63.158 0.00 0.00 0.00 6.13
1180 1391 1.313812 CCTCGAAGACTGTACCGGCT 61.314 60.000 0.00 0.00 0.00 5.52
1183 1394 1.592400 CGAAGACTGTACCGGCTGGA 61.592 60.000 21.41 0.00 39.21 3.86
1184 1395 0.108756 GAAGACTGTACCGGCTGGAC 60.109 60.000 21.41 12.73 39.21 4.02
1185 1396 1.874345 AAGACTGTACCGGCTGGACG 61.874 60.000 21.41 10.65 39.21 4.79
1186 1397 2.599578 ACTGTACCGGCTGGACGT 60.600 61.111 21.41 11.23 39.21 4.34
1187 1398 2.126071 CTGTACCGGCTGGACGTG 60.126 66.667 21.41 5.70 39.21 4.49
1188 1399 4.367023 TGTACCGGCTGGACGTGC 62.367 66.667 21.41 0.00 39.21 5.34
1189 1400 4.065281 GTACCGGCTGGACGTGCT 62.065 66.667 21.41 0.00 39.21 4.40
1190 1401 3.755628 TACCGGCTGGACGTGCTC 61.756 66.667 21.41 0.00 39.21 4.26
1198 1409 3.567473 GGACGTGCTCCAAGAAGC 58.433 61.111 0.00 0.00 42.82 3.86
1205 1419 0.326264 TGCTCCAAGAAGCCTCCTTC 59.674 55.000 0.00 0.00 46.29 3.46
1211 1425 1.065854 CAAGAAGCCTCCTTCCGTGAT 60.066 52.381 0.17 0.00 46.97 3.06
1247 1461 2.498481 CTGTCAACCCCGGTGAGTTATA 59.502 50.000 0.00 0.00 0.00 0.98
1249 1463 3.133362 TGTCAACCCCGGTGAGTTATATC 59.867 47.826 0.00 0.00 0.00 1.63
1250 1464 2.363038 TCAACCCCGGTGAGTTATATCG 59.637 50.000 0.00 0.00 0.00 2.92
1252 1466 2.391678 ACCCCGGTGAGTTATATCGTT 58.608 47.619 0.00 0.00 0.00 3.85
1254 1468 2.288640 CCCCGGTGAGTTATATCGTTCC 60.289 54.545 0.00 0.00 0.00 3.62
1255 1469 2.288640 CCCGGTGAGTTATATCGTTCCC 60.289 54.545 0.00 0.00 0.00 3.97
1256 1470 2.606308 CCGGTGAGTTATATCGTTCCCG 60.606 54.545 0.00 0.00 0.00 5.14
1257 1471 2.401351 GGTGAGTTATATCGTTCCCGC 58.599 52.381 0.00 0.00 0.00 6.13
1258 1472 2.049228 GTGAGTTATATCGTTCCCGCG 58.951 52.381 0.00 0.00 0.00 6.46
1259 1473 1.677576 TGAGTTATATCGTTCCCGCGT 59.322 47.619 4.92 0.00 0.00 6.01
1260 1474 2.099592 TGAGTTATATCGTTCCCGCGTT 59.900 45.455 4.92 0.00 0.00 4.84
1261 1475 3.314913 TGAGTTATATCGTTCCCGCGTTA 59.685 43.478 4.92 0.00 0.00 3.18
1262 1476 3.893720 AGTTATATCGTTCCCGCGTTAG 58.106 45.455 4.92 0.00 0.00 2.34
1263 1477 3.565482 AGTTATATCGTTCCCGCGTTAGA 59.435 43.478 4.92 0.00 0.00 2.10
1264 1478 2.701073 ATATCGTTCCCGCGTTAGAG 57.299 50.000 4.92 0.00 0.00 2.43
1266 1480 1.664321 ATCGTTCCCGCGTTAGAGCT 61.664 55.000 4.92 0.00 34.40 4.09
1269 1483 0.802607 GTTCCCGCGTTAGAGCTCAG 60.803 60.000 17.77 5.34 34.40 3.35
1276 1490 1.623359 CGTTAGAGCTCAGTGTCAGC 58.377 55.000 17.77 0.00 37.12 4.26
1294 1508 3.118149 TCAGCTGCCTGATCATGTATGTT 60.118 43.478 9.47 0.00 42.98 2.71
1295 1509 4.101430 TCAGCTGCCTGATCATGTATGTTA 59.899 41.667 9.47 0.00 42.98 2.41
1297 1511 4.102210 AGCTGCCTGATCATGTATGTTAGT 59.898 41.667 0.00 0.00 0.00 2.24
1298 1512 4.212847 GCTGCCTGATCATGTATGTTAGTG 59.787 45.833 0.00 0.00 0.00 2.74
1299 1513 5.357742 TGCCTGATCATGTATGTTAGTGT 57.642 39.130 0.00 0.00 0.00 3.55
1300 1514 6.478512 TGCCTGATCATGTATGTTAGTGTA 57.521 37.500 0.00 0.00 0.00 2.90
1301 1515 7.066307 TGCCTGATCATGTATGTTAGTGTAT 57.934 36.000 0.00 0.00 0.00 2.29
1302 1516 6.930722 TGCCTGATCATGTATGTTAGTGTATG 59.069 38.462 0.00 0.00 0.00 2.39
1303 1517 6.931281 GCCTGATCATGTATGTTAGTGTATGT 59.069 38.462 0.00 0.00 0.00 2.29
1304 1518 7.095481 GCCTGATCATGTATGTTAGTGTATGTG 60.095 40.741 0.00 0.00 0.00 3.21
1305 1519 7.928167 CCTGATCATGTATGTTAGTGTATGTGT 59.072 37.037 0.00 0.00 0.00 3.72
1306 1520 9.965824 CTGATCATGTATGTTAGTGTATGTGTA 57.034 33.333 0.00 0.00 0.00 2.90
1318 1532 4.980434 AGTGTATGTGTAGTTCGTGTGTTC 59.020 41.667 0.00 0.00 0.00 3.18
1321 1535 3.088194 TGTGTAGTTCGTGTGTTCTCC 57.912 47.619 0.00 0.00 0.00 3.71
1326 1540 0.232303 GTTCGTGTGTTCTCCGCAAG 59.768 55.000 0.00 0.00 34.80 4.01
1346 1560 3.950397 AGTTTGTTTGTCTGACCTGTCA 58.050 40.909 5.17 0.00 38.06 3.58
1352 1566 3.804786 TTGTCTGACCTGTCACGTTTA 57.195 42.857 5.17 0.00 35.46 2.01
1355 1569 2.033372 TCTGACCTGTCACGTTTACCA 58.967 47.619 0.00 0.00 35.46 3.25
1436 1650 1.521457 GCCGATCATGGCGAGTTCA 60.521 57.895 9.90 0.00 46.75 3.18
1454 1668 0.607217 CAACATCACTGAGGGCAGCA 60.607 55.000 0.00 0.00 46.26 4.41
1496 1710 1.006825 CGATCACGGCGACTTCAACA 61.007 55.000 16.62 0.00 35.72 3.33
1498 1712 0.033504 ATCACGGCGACTTCAACACT 59.966 50.000 16.62 0.00 0.00 3.55
1501 1715 2.243957 CGGCGACTTCAACACTGCA 61.244 57.895 0.00 0.00 0.00 4.41
1596 1810 3.637694 GGTATAGGCCGAGAAACTCTTCT 59.362 47.826 0.00 0.00 44.93 2.85
1597 1811 4.826183 GGTATAGGCCGAGAAACTCTTCTA 59.174 45.833 0.00 0.00 42.19 2.10
1598 1812 5.477637 GGTATAGGCCGAGAAACTCTTCTAT 59.522 44.000 0.00 0.00 42.19 1.98
1600 1814 4.922471 AGGCCGAGAAACTCTTCTATAC 57.078 45.455 0.00 0.00 42.19 1.47
1601 1815 4.538738 AGGCCGAGAAACTCTTCTATACT 58.461 43.478 0.00 0.00 42.19 2.12
1603 1817 5.532032 AGGCCGAGAAACTCTTCTATACTAC 59.468 44.000 0.00 0.00 42.19 2.73
1604 1818 5.532032 GGCCGAGAAACTCTTCTATACTACT 59.468 44.000 0.00 0.00 42.19 2.57
1605 1819 6.709846 GGCCGAGAAACTCTTCTATACTACTA 59.290 42.308 0.00 0.00 42.19 1.82
1606 1820 7.391275 GGCCGAGAAACTCTTCTATACTACTAT 59.609 40.741 0.00 0.00 42.19 2.12
1607 1821 8.785946 GCCGAGAAACTCTTCTATACTACTATT 58.214 37.037 0.00 0.00 42.19 1.73
2180 3652 2.670148 GGGTCTTCTCCGCCACCAT 61.670 63.158 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 56 6.454981 CGGTTTTGATTGACTTTTGGTGTTTC 60.455 38.462 0.00 0.00 0.00 2.78
62 67 5.221891 CGATGAATCGGTTTTGATTGACT 57.778 39.130 4.77 0.00 45.93 3.41
81 86 4.270084 TGATATTCTTCTTTTTCGCGCGAT 59.730 37.500 35.21 16.95 0.00 4.58
100 106 1.948104 CAGCCGGAACCGATTTGATA 58.052 50.000 15.07 0.00 42.83 2.15
130 136 1.194781 ACTGGACAGGGAGAATGCGT 61.195 55.000 4.14 0.00 0.00 5.24
174 190 5.420409 CAGTTGGTAACTAAGACCATCTCC 58.580 45.833 3.02 0.00 46.29 3.71
185 201 8.215050 TCTTCTTTGAAATCCAGTTGGTAACTA 58.785 33.333 0.00 0.00 40.46 2.24
231 251 1.048601 TGAGGAAACGCTGGTTCTCT 58.951 50.000 6.35 2.91 34.62 3.10
232 252 1.878953 TTGAGGAAACGCTGGTTCTC 58.121 50.000 6.35 3.77 34.62 2.87
233 253 2.341846 TTTGAGGAAACGCTGGTTCT 57.658 45.000 6.35 0.00 34.62 3.01
401 448 8.764524 ATCTAATCTAATCCAACTTATGCGTC 57.235 34.615 0.00 0.00 0.00 5.19
489 550 0.108615 CTAGGAGCAGGTGAACCGTG 60.109 60.000 0.00 0.00 42.08 4.94
490 551 1.258445 CCTAGGAGCAGGTGAACCGT 61.258 60.000 1.05 0.00 42.08 4.83
491 552 0.970937 TCCTAGGAGCAGGTGAACCG 60.971 60.000 7.62 0.00 42.08 4.44
492 553 1.501582 ATCCTAGGAGCAGGTGAACC 58.498 55.000 18.34 0.00 36.99 3.62
494 555 2.307768 CGTATCCTAGGAGCAGGTGAA 58.692 52.381 18.34 0.00 36.99 3.18
495 556 1.214673 ACGTATCCTAGGAGCAGGTGA 59.785 52.381 18.34 0.00 36.99 4.02
609 677 0.111061 AGGCATGCAACCTCTGAACA 59.889 50.000 21.36 0.00 28.76 3.18
610 678 0.524862 CAGGCATGCAACCTCTGAAC 59.475 55.000 21.36 0.00 34.42 3.18
635 703 3.809832 CCAGATTACTAGATTTGGCACCG 59.190 47.826 0.00 0.00 0.00 4.94
665 734 1.303970 GCTCTTCTTGGCAAGGGCT 60.304 57.895 25.92 0.00 45.23 5.19
735 808 5.642063 GGATTAGTGTTCAAGTTGGATTCGA 59.358 40.000 2.34 0.00 0.00 3.71
736 809 5.643777 AGGATTAGTGTTCAAGTTGGATTCG 59.356 40.000 2.34 0.00 0.00 3.34
737 810 6.623767 GCAGGATTAGTGTTCAAGTTGGATTC 60.624 42.308 2.34 0.00 0.00 2.52
739 812 4.702131 GCAGGATTAGTGTTCAAGTTGGAT 59.298 41.667 2.34 0.00 0.00 3.41
757 830 4.436332 CGCTTGCTATGATATATGCAGGA 58.564 43.478 8.51 0.00 35.04 3.86
758 831 3.558829 CCGCTTGCTATGATATATGCAGG 59.441 47.826 0.00 0.00 36.75 4.85
759 832 4.186926 ACCGCTTGCTATGATATATGCAG 58.813 43.478 0.00 0.00 36.75 4.41
762 835 7.595311 TTGTTACCGCTTGCTATGATATATG 57.405 36.000 0.00 0.00 0.00 1.78
765 838 5.049405 GCTTTGTTACCGCTTGCTATGATAT 60.049 40.000 0.00 0.00 0.00 1.63
766 839 4.272504 GCTTTGTTACCGCTTGCTATGATA 59.727 41.667 0.00 0.00 0.00 2.15
767 840 3.065371 GCTTTGTTACCGCTTGCTATGAT 59.935 43.478 0.00 0.00 0.00 2.45
768 841 2.418628 GCTTTGTTACCGCTTGCTATGA 59.581 45.455 0.00 0.00 0.00 2.15
769 842 2.420022 AGCTTTGTTACCGCTTGCTATG 59.580 45.455 0.00 0.00 0.00 2.23
779 868 1.804601 ACCGCACTAGCTTTGTTACC 58.195 50.000 0.00 0.00 39.10 2.85
827 916 4.508128 ATCGGTGCGCGTCGGATT 62.508 61.111 19.25 5.25 0.00 3.01
841 930 0.591488 TTTCGCGGACTGATCGATCG 60.591 55.000 20.03 9.36 31.96 3.69
863 1064 1.237285 GCCGCACTGTTCATCCACTT 61.237 55.000 0.00 0.00 0.00 3.16
884 1085 2.069273 CCTGAATTTATAGCCGAGCGG 58.931 52.381 4.20 4.20 38.57 5.52
889 1090 0.517316 GGCGCCTGAATTTATAGCCG 59.483 55.000 22.15 0.00 33.43 5.52
932 1137 2.933287 TGGTAGGCAGTGGGGGTG 60.933 66.667 0.00 0.00 0.00 4.61
934 1139 1.306654 TACTGGTAGGCAGTGGGGG 60.307 63.158 0.00 0.00 34.38 5.40
941 1146 1.278127 GGAAAGTGCTACTGGTAGGCA 59.722 52.381 9.43 5.63 33.87 4.75
942 1147 1.407025 GGGAAAGTGCTACTGGTAGGC 60.407 57.143 9.43 3.45 33.87 3.93
954 1159 1.949525 CACACTGGAACTGGGAAAGTG 59.050 52.381 0.00 0.00 43.07 3.16
955 1160 1.843851 TCACACTGGAACTGGGAAAGT 59.156 47.619 0.00 0.00 42.60 2.66
958 1163 1.416401 GAGTCACACTGGAACTGGGAA 59.584 52.381 0.00 0.00 33.79 3.97
963 1168 1.007271 CGCGAGTCACACTGGAACT 60.007 57.895 0.00 0.00 0.00 3.01
964 1169 1.004277 CTCGCGAGTCACACTGGAAC 61.004 60.000 27.79 0.00 0.00 3.62
965 1170 1.285950 CTCGCGAGTCACACTGGAA 59.714 57.895 27.79 0.00 0.00 3.53
966 1171 2.954611 CTCGCGAGTCACACTGGA 59.045 61.111 27.79 0.00 0.00 3.86
967 1172 2.807045 GCTCGCGAGTCACACTGG 60.807 66.667 34.46 9.89 0.00 4.00
968 1173 1.799519 GAGCTCGCGAGTCACACTG 60.800 63.158 34.46 10.65 0.00 3.66
969 1174 2.563942 GAGCTCGCGAGTCACACT 59.436 61.111 34.46 23.29 0.00 3.55
987 1192 4.299316 GCCATTGCGCGATCGGTC 62.299 66.667 18.30 12.74 35.95 4.79
1026 1231 2.441532 ATCAGCATGGCCAGCACC 60.442 61.111 23.46 8.00 36.16 5.01
1028 1233 1.153025 GAGATCAGCATGGCCAGCA 60.153 57.895 23.46 9.09 36.16 4.41
1029 1234 1.897615 GGAGATCAGCATGGCCAGC 60.898 63.158 13.05 15.25 36.16 4.85
1030 1235 0.183014 AAGGAGATCAGCATGGCCAG 59.817 55.000 13.05 4.54 36.16 4.85
1065 1270 1.376812 GAAATCGGACCCCAGCGTT 60.377 57.895 0.00 0.00 0.00 4.84
1068 1273 3.202706 GCGAAATCGGACCCCAGC 61.203 66.667 4.84 0.00 40.23 4.85
1069 1274 2.513897 GGCGAAATCGGACCCCAG 60.514 66.667 4.84 0.00 40.23 4.45
1070 1275 4.460683 CGGCGAAATCGGACCCCA 62.461 66.667 0.00 0.00 40.23 4.96
1087 1292 3.423154 GTGGTGGCAGTAGCACGC 61.423 66.667 0.00 0.00 44.61 5.34
1089 1294 0.817634 TGTTGTGGTGGCAGTAGCAC 60.818 55.000 9.39 9.39 46.35 4.40
1099 1304 1.627879 GTGCACACTTTGTTGTGGTG 58.372 50.000 13.17 0.00 46.00 4.17
1100 1305 0.170116 CGTGCACACTTTGTTGTGGT 59.830 50.000 18.64 0.00 46.00 4.16
1101 1306 0.449786 TCGTGCACACTTTGTTGTGG 59.550 50.000 18.64 0.00 46.00 4.17
1103 1308 2.030717 TGTTTCGTGCACACTTTGTTGT 60.031 40.909 18.64 0.00 0.00 3.32
1105 1310 2.999507 TGTTTCGTGCACACTTTGTT 57.000 40.000 18.64 0.00 0.00 2.83
1110 1315 0.030638 GCCATTGTTTCGTGCACACT 59.969 50.000 18.64 0.00 0.00 3.55
1111 1316 0.939106 GGCCATTGTTTCGTGCACAC 60.939 55.000 18.64 8.30 0.00 3.82
1112 1317 1.361993 GGCCATTGTTTCGTGCACA 59.638 52.632 18.64 0.81 0.00 4.57
1117 1322 1.729470 TTGCGTGGCCATTGTTTCGT 61.729 50.000 9.72 0.00 0.00 3.85
1118 1323 1.003262 CTTGCGTGGCCATTGTTTCG 61.003 55.000 9.72 7.94 0.00 3.46
1119 1324 1.284297 GCTTGCGTGGCCATTGTTTC 61.284 55.000 9.72 0.00 0.00 2.78
1135 1346 0.036164 TTCATGCAGTACACCGGCTT 59.964 50.000 0.00 0.00 0.00 4.35
1137 1348 0.391130 TCTTCATGCAGTACACCGGC 60.391 55.000 0.00 0.00 0.00 6.13
1139 1350 3.667960 GCTTTTCTTCATGCAGTACACCG 60.668 47.826 0.00 0.00 0.00 4.94
1140 1351 3.366374 GGCTTTTCTTCATGCAGTACACC 60.366 47.826 0.00 0.00 0.00 4.16
1143 1354 3.181516 CGAGGCTTTTCTTCATGCAGTAC 60.182 47.826 0.00 0.00 0.00 2.73
1144 1355 3.002791 CGAGGCTTTTCTTCATGCAGTA 58.997 45.455 0.00 0.00 0.00 2.74
1145 1356 1.808945 CGAGGCTTTTCTTCATGCAGT 59.191 47.619 0.00 0.00 0.00 4.40
1153 1364 3.477210 ACAGTCTTCGAGGCTTTTCTT 57.523 42.857 0.00 0.00 0.00 2.52
1165 1376 0.108756 GTCCAGCCGGTACAGTCTTC 60.109 60.000 1.90 0.00 0.00 2.87
1167 1378 2.341101 CGTCCAGCCGGTACAGTCT 61.341 63.158 1.90 0.00 0.00 3.24
1168 1379 2.181021 CGTCCAGCCGGTACAGTC 59.819 66.667 1.90 0.00 0.00 3.51
1170 1381 2.126071 CACGTCCAGCCGGTACAG 60.126 66.667 1.90 0.00 0.00 2.74
1183 1394 1.004440 GAGGCTTCTTGGAGCACGT 60.004 57.895 3.11 0.00 44.49 4.49
1184 1395 1.743252 GGAGGCTTCTTGGAGCACG 60.743 63.158 3.11 0.00 44.49 5.34
1185 1396 0.037447 AAGGAGGCTTCTTGGAGCAC 59.963 55.000 7.40 0.00 44.49 4.40
1186 1397 0.326264 GAAGGAGGCTTCTTGGAGCA 59.674 55.000 14.10 0.00 44.49 4.26
1187 1398 0.393673 GGAAGGAGGCTTCTTGGAGC 60.394 60.000 14.10 0.00 41.96 4.70
1188 1399 0.107945 CGGAAGGAGGCTTCTTGGAG 60.108 60.000 14.10 0.00 34.06 3.86
1189 1400 0.836400 ACGGAAGGAGGCTTCTTGGA 60.836 55.000 14.10 0.00 34.06 3.53
1190 1401 0.674895 CACGGAAGGAGGCTTCTTGG 60.675 60.000 14.10 7.21 34.06 3.61
1191 1402 0.321671 TCACGGAAGGAGGCTTCTTG 59.678 55.000 14.10 1.64 34.06 3.02
1193 1404 0.539051 CATCACGGAAGGAGGCTTCT 59.461 55.000 0.00 0.00 34.06 2.85
1194 1405 1.092345 GCATCACGGAAGGAGGCTTC 61.092 60.000 0.00 0.00 38.88 3.86
1195 1406 1.078143 GCATCACGGAAGGAGGCTT 60.078 57.895 0.00 0.00 38.88 4.35
1196 1407 2.586792 GCATCACGGAAGGAGGCT 59.413 61.111 0.00 0.00 38.88 4.58
1197 1408 2.514824 GGCATCACGGAAGGAGGC 60.515 66.667 0.00 0.00 41.04 4.70
1198 1409 1.450312 GTGGCATCACGGAAGGAGG 60.450 63.158 0.00 0.00 33.87 4.30
1225 1439 2.358737 CTCACCGGGGTTGACAGC 60.359 66.667 2.12 0.00 0.00 4.40
1226 1440 0.682852 TAACTCACCGGGGTTGACAG 59.317 55.000 2.12 0.00 0.00 3.51
1250 1464 0.802607 CTGAGCTCTAACGCGGGAAC 60.803 60.000 16.19 0.98 34.40 3.62
1252 1466 1.677966 ACTGAGCTCTAACGCGGGA 60.678 57.895 16.19 4.70 34.40 5.14
1254 1468 0.798771 GACACTGAGCTCTAACGCGG 60.799 60.000 16.19 0.00 34.40 6.46
1255 1469 0.109735 TGACACTGAGCTCTAACGCG 60.110 55.000 16.19 3.53 34.40 6.01
1256 1470 1.623359 CTGACACTGAGCTCTAACGC 58.377 55.000 16.19 2.52 0.00 4.84
1257 1471 1.201181 AGCTGACACTGAGCTCTAACG 59.799 52.381 16.19 3.44 43.54 3.18
1258 1472 2.605030 CAGCTGACACTGAGCTCTAAC 58.395 52.381 16.19 2.96 45.24 2.34
1259 1473 1.067283 GCAGCTGACACTGAGCTCTAA 60.067 52.381 20.43 0.00 45.24 2.10
1260 1474 0.529833 GCAGCTGACACTGAGCTCTA 59.470 55.000 20.43 0.24 45.24 2.43
1261 1475 1.292860 GCAGCTGACACTGAGCTCT 59.707 57.895 20.43 0.00 45.24 4.09
1262 1476 1.741032 GGCAGCTGACACTGAGCTC 60.741 63.158 20.43 6.82 45.24 4.09
1264 1478 2.033755 CAGGCAGCTGACACTGAGC 61.034 63.158 24.55 0.13 40.25 4.26
1266 1480 0.248565 GATCAGGCAGCTGACACTGA 59.751 55.000 27.19 27.19 43.33 3.41
1269 1483 1.015109 CATGATCAGGCAGCTGACAC 58.985 55.000 24.55 10.60 36.05 3.67
1276 1490 5.363101 ACACTAACATACATGATCAGGCAG 58.637 41.667 7.40 0.00 0.00 4.85
1279 1493 7.928167 ACACATACACTAACATACATGATCAGG 59.072 37.037 5.68 5.68 0.00 3.86
1284 1498 9.797556 GAACTACACATACACTAACATACATGA 57.202 33.333 0.00 0.00 0.00 3.07
1291 1505 5.916320 CACACGAACTACACATACACTAACA 59.084 40.000 0.00 0.00 0.00 2.41
1294 1508 5.694231 ACACACGAACTACACATACACTA 57.306 39.130 0.00 0.00 0.00 2.74
1295 1509 4.579454 ACACACGAACTACACATACACT 57.421 40.909 0.00 0.00 0.00 3.55
1297 1511 5.190992 AGAACACACGAACTACACATACA 57.809 39.130 0.00 0.00 0.00 2.29
1298 1512 4.620184 GGAGAACACACGAACTACACATAC 59.380 45.833 0.00 0.00 0.00 2.39
1299 1513 4.614306 CGGAGAACACACGAACTACACATA 60.614 45.833 0.00 0.00 0.00 2.29
1300 1514 3.650139 GGAGAACACACGAACTACACAT 58.350 45.455 0.00 0.00 0.00 3.21
1301 1515 2.542205 CGGAGAACACACGAACTACACA 60.542 50.000 0.00 0.00 0.00 3.72
1302 1516 2.049228 CGGAGAACACACGAACTACAC 58.951 52.381 0.00 0.00 0.00 2.90
1303 1517 1.601162 GCGGAGAACACACGAACTACA 60.601 52.381 0.00 0.00 0.00 2.74
1304 1518 1.058404 GCGGAGAACACACGAACTAC 58.942 55.000 0.00 0.00 0.00 2.73
1305 1519 0.669619 TGCGGAGAACACACGAACTA 59.330 50.000 0.00 0.00 0.00 2.24
1306 1520 0.179094 TTGCGGAGAACACACGAACT 60.179 50.000 0.00 0.00 0.00 3.01
1318 1532 2.354510 TCAGACAAACAAACTTGCGGAG 59.645 45.455 0.00 0.00 0.00 4.63
1321 1535 2.097466 AGGTCAGACAAACAAACTTGCG 59.903 45.455 2.17 0.00 0.00 4.85
1326 1540 3.485216 CGTGACAGGTCAGACAAACAAAC 60.485 47.826 1.66 0.00 40.75 2.93
1346 1560 1.000717 GCAGCAAACCATGGTAAACGT 60.001 47.619 20.12 0.00 37.77 3.99
1352 1566 1.274167 CATTCAGCAGCAAACCATGGT 59.726 47.619 13.00 13.00 41.41 3.55
1355 1569 3.826637 GCATTCAGCAGCAAACCAT 57.173 47.368 0.00 0.00 44.79 3.55
1426 1640 1.069978 TCAGTGATGTTGAACTCGCCA 59.930 47.619 0.00 0.00 0.00 5.69
1436 1650 0.330604 ATGCTGCCCTCAGTGATGTT 59.669 50.000 0.00 0.00 42.29 2.71
1489 1703 3.117491 TCCTCTTCTGCAGTGTTGAAG 57.883 47.619 14.67 9.88 38.69 3.02
1498 1712 0.107800 GAGCTGCATCCTCTTCTGCA 60.108 55.000 1.02 0.00 45.60 4.41
1501 1715 0.975040 ACGGAGCTGCATCCTCTTCT 60.975 55.000 5.91 0.00 37.20 2.85
1529 1743 2.364842 TCTCCAGCCAGCCTCTCC 60.365 66.667 0.00 0.00 0.00 3.71
1903 3366 0.695803 AGGGGAGAGCTATGGTTGGG 60.696 60.000 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.