Multiple sequence alignment - TraesCS7B01G018500

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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 TraesCS7B01G018500 chr7B 100.000 3817 0 0 1 3817 15590139 15586323 0.000000e+00 7049.0
1 TraesCS7B01G018500 chr7D 94.786 1400 66 4 1509 2903 72950667 72952064 0.000000e+00 2174.0
2 TraesCS7B01G018500 chr7D 91.081 583 40 9 1 578 72949145 72949720 0.000000e+00 778.0
3 TraesCS7B01G018500 chr7D 91.063 414 29 4 614 1020 72949720 72950132 1.550000e-153 553.0
4 TraesCS7B01G018500 chr7D 90.441 408 20 8 1073 1479 72950152 72950541 1.570000e-143 520.0
5 TraesCS7B01G018500 chr7A 90.669 1436 76 23 1480 2903 77430918 77429529 0.000000e+00 1857.0
6 TraesCS7B01G018500 chr7A 83.874 924 147 2 2896 3817 97870951 97870028 0.000000e+00 880.0
7 TraesCS7B01G018500 chr7A 82.866 928 149 9 2896 3817 214301306 214300383 0.000000e+00 824.0
8 TraesCS7B01G018500 chr7A 92.055 579 38 7 1 576 77432519 77431946 0.000000e+00 808.0
9 TraesCS7B01G018500 chr7A 89.311 421 24 11 1073 1492 77431376 77430976 3.400000e-140 508.0
10 TraesCS7B01G018500 chr7A 91.642 335 19 5 546 872 77431916 77431583 4.490000e-124 455.0
11 TraesCS7B01G018500 chr7A 86.905 168 17 4 857 1020 77431562 77431396 2.340000e-42 183.0
12 TraesCS7B01G018500 chr5B 94.366 923 42 4 2896 3817 692224466 692225379 0.000000e+00 1408.0
13 TraesCS7B01G018500 chr5D 93.450 916 50 4 2896 3810 193138429 193139335 0.000000e+00 1351.0
14 TraesCS7B01G018500 chr6A 91.328 738 62 2 3080 3817 72620954 72620219 0.000000e+00 1007.0
15 TraesCS7B01G018500 chr2A 93.967 663 39 1 3156 3817 291313704 291313042 0.000000e+00 1002.0
16 TraesCS7B01G018500 chr1A 84.056 922 146 1 2896 3817 550451005 550450085 0.000000e+00 887.0
17 TraesCS7B01G018500 chr3A 83.931 921 139 6 2897 3817 208399866 208400777 0.000000e+00 872.0
18 TraesCS7B01G018500 chr4B 83.152 920 148 5 2898 3817 338433048 338432136 0.000000e+00 833.0
19 TraesCS7B01G018500 chr4D 96.875 32 1 0 546 577 243073968 243073999 2.000000e-03 54.7


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 TraesCS7B01G018500 chr7B 15586323 15590139 3816 True 7049.00 7049 100.00000 1 3817 1 chr7B.!!$R1 3816
1 TraesCS7B01G018500 chr7D 72949145 72952064 2919 False 1006.25 2174 91.84275 1 2903 4 chr7D.!!$F1 2902
2 TraesCS7B01G018500 chr7A 97870028 97870951 923 True 880.00 880 83.87400 2896 3817 1 chr7A.!!$R1 921
3 TraesCS7B01G018500 chr7A 214300383 214301306 923 True 824.00 824 82.86600 2896 3817 1 chr7A.!!$R2 921
4 TraesCS7B01G018500 chr7A 77429529 77432519 2990 True 762.20 1857 90.11640 1 2903 5 chr7A.!!$R3 2902
5 TraesCS7B01G018500 chr5B 692224466 692225379 913 False 1408.00 1408 94.36600 2896 3817 1 chr5B.!!$F1 921
6 TraesCS7B01G018500 chr5D 193138429 193139335 906 False 1351.00 1351 93.45000 2896 3810 1 chr5D.!!$F1 914
7 TraesCS7B01G018500 chr6A 72620219 72620954 735 True 1007.00 1007 91.32800 3080 3817 1 chr6A.!!$R1 737
8 TraesCS7B01G018500 chr2A 291313042 291313704 662 True 1002.00 1002 93.96700 3156 3817 1 chr2A.!!$R1 661
9 TraesCS7B01G018500 chr1A 550450085 550451005 920 True 887.00 887 84.05600 2896 3817 1 chr1A.!!$R1 921
10 TraesCS7B01G018500 chr3A 208399866 208400777 911 False 872.00 872 83.93100 2897 3817 1 chr3A.!!$F1 920
11 TraesCS7B01G018500 chr4B 338432136 338433048 912 True 833.00 833 83.15200 2898 3817 1 chr4B.!!$R1 919

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
610 712 0.107643 TTGTGTTGAGATGGTGCCGA 59.892 50.0 0.0 0.0 0.0 5.54 F
1022 1178 0.254178 ATTCTCATTGCCTGGACGCT 59.746 50.0 0.0 0.0 0.0 5.07 F
1029 1185 0.326595 TTGCCTGGACGCTGGATTAA 59.673 50.0 0.0 0.0 0.0 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 1624 0.037139 AACTAATGGTGCCACGCGTA 60.037 50.0 13.44 0.0 0.0 4.42 R
2601 2874 0.405973 GGCTTTCTCACCCCCTTCTT 59.594 55.0 0.00 0.0 0.0 2.52 R
2988 3290 1.254284 ACGCCTCCTCTTCCTCTGTG 61.254 60.0 0.00 0.0 0.0 3.66 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
34 36 9.634163 CCTCACCCTTTATGTGTTTTAAAATAC 57.366 33.333 17.98 17.98 35.25 1.89
85 89 1.959710 TGCCCTCCAACCATAGTGTA 58.040 50.000 0.00 0.00 0.00 2.90
86 90 2.487775 TGCCCTCCAACCATAGTGTAT 58.512 47.619 0.00 0.00 0.00 2.29
91 95 5.045578 GCCCTCCAACCATAGTGTATATCAT 60.046 44.000 0.00 0.00 0.00 2.45
101 105 8.874156 ACCATAGTGTATATCATCAAGTCACAT 58.126 33.333 0.00 0.00 0.00 3.21
111 115 7.731882 ATCATCAAGTCACATCATTGATCTC 57.268 36.000 0.00 0.00 40.71 2.75
112 116 6.646267 TCATCAAGTCACATCATTGATCTCA 58.354 36.000 0.00 0.00 40.71 3.27
113 117 7.107542 TCATCAAGTCACATCATTGATCTCAA 58.892 34.615 0.00 0.00 40.71 3.02
114 118 6.980051 TCAAGTCACATCATTGATCTCAAG 57.020 37.500 0.00 0.00 39.47 3.02
115 119 6.704310 TCAAGTCACATCATTGATCTCAAGA 58.296 36.000 0.00 0.00 39.47 3.02
116 120 7.163441 TCAAGTCACATCATTGATCTCAAGAA 58.837 34.615 0.00 0.00 39.47 2.52
248 253 5.681639 AGTATTTAGGGCCTCATGTAACAC 58.318 41.667 10.74 0.00 0.00 3.32
271 277 6.672218 CACCACCACTCCCTCCATAATATATA 59.328 42.308 0.00 0.00 0.00 0.86
331 338 3.344515 GGTTTGATCACCCTACTCAACC 58.655 50.000 0.00 0.00 0.00 3.77
341 348 3.261897 ACCCTACTCAACCTGTTCATCAG 59.738 47.826 0.00 0.00 43.27 2.90
350 357 3.077359 ACCTGTTCATCAGCACTTTAGC 58.923 45.455 0.00 0.00 42.38 3.09
411 418 7.640240 GGTCTAAATTTTTGTATCTGCTTAGCG 59.360 37.037 0.00 0.00 0.00 4.26
523 530 3.330405 TGAGACCCCATTTCACAAGATCA 59.670 43.478 0.00 0.00 0.00 2.92
542 549 9.552114 CAAGATCACAGAAATGTTGATAGAAAC 57.448 33.333 0.00 0.00 31.01 2.78
547 554 8.352201 TCACAGAAATGTTGATAGAAACCTTTG 58.648 33.333 0.00 0.00 30.93 2.77
549 556 7.014615 ACAGAAATGTTGATAGAAACCTTTGCT 59.985 33.333 0.00 0.00 30.93 3.91
550 557 7.327761 CAGAAATGTTGATAGAAACCTTTGCTG 59.672 37.037 0.00 0.00 30.93 4.41
551 558 4.503741 TGTTGATAGAAACCTTTGCTGC 57.496 40.909 0.00 0.00 0.00 5.25
578 680 1.126079 GTTGTCGTCGTCGTTGTCAT 58.874 50.000 1.33 0.00 38.33 3.06
579 681 1.125270 TTGTCGTCGTCGTTGTCATG 58.875 50.000 1.33 0.00 38.33 3.07
580 682 0.662077 TGTCGTCGTCGTTGTCATGG 60.662 55.000 1.33 0.00 38.33 3.66
581 683 1.731613 TCGTCGTCGTTGTCATGGC 60.732 57.895 1.33 0.00 38.33 4.40
582 684 2.019408 CGTCGTCGTTGTCATGGCA 61.019 57.895 0.00 0.00 0.00 4.92
583 685 1.553195 CGTCGTCGTTGTCATGGCAA 61.553 55.000 9.09 9.09 0.00 4.52
584 686 0.796312 GTCGTCGTTGTCATGGCAAT 59.204 50.000 17.07 0.00 0.00 3.56
585 687 0.795698 TCGTCGTTGTCATGGCAATG 59.204 50.000 23.46 23.46 36.87 2.82
586 688 0.179192 CGTCGTTGTCATGGCAATGG 60.179 55.000 27.41 17.50 36.37 3.16
587 689 0.881118 GTCGTTGTCATGGCAATGGT 59.119 50.000 27.41 0.00 36.37 3.55
588 690 2.080693 GTCGTTGTCATGGCAATGGTA 58.919 47.619 27.41 10.48 36.37 3.25
589 691 2.486203 GTCGTTGTCATGGCAATGGTAA 59.514 45.455 27.41 9.80 36.37 2.85
590 692 2.486203 TCGTTGTCATGGCAATGGTAAC 59.514 45.455 27.41 9.64 36.37 2.50
591 693 2.487762 CGTTGTCATGGCAATGGTAACT 59.512 45.455 22.07 0.00 34.30 2.24
592 694 3.057596 CGTTGTCATGGCAATGGTAACTT 60.058 43.478 22.07 0.00 34.30 2.66
593 695 4.236935 GTTGTCATGGCAATGGTAACTTG 58.763 43.478 17.07 0.00 34.30 3.16
594 696 3.495331 TGTCATGGCAATGGTAACTTGT 58.505 40.909 0.00 0.00 34.30 3.16
595 697 3.255395 TGTCATGGCAATGGTAACTTGTG 59.745 43.478 0.00 0.00 34.30 3.33
596 698 3.255642 GTCATGGCAATGGTAACTTGTGT 59.744 43.478 0.00 0.00 34.30 3.72
597 699 3.894427 TCATGGCAATGGTAACTTGTGTT 59.106 39.130 0.00 0.00 36.04 3.32
598 700 3.724508 TGGCAATGGTAACTTGTGTTG 57.275 42.857 0.00 0.00 37.59 3.33
599 701 3.291584 TGGCAATGGTAACTTGTGTTGA 58.708 40.909 0.00 0.00 37.59 3.18
600 702 3.317711 TGGCAATGGTAACTTGTGTTGAG 59.682 43.478 0.00 0.00 37.59 3.02
601 703 3.568007 GGCAATGGTAACTTGTGTTGAGA 59.432 43.478 0.00 0.00 37.59 3.27
602 704 4.218417 GGCAATGGTAACTTGTGTTGAGAT 59.782 41.667 0.00 0.00 37.59 2.75
603 705 5.156355 GCAATGGTAACTTGTGTTGAGATG 58.844 41.667 0.00 0.00 37.59 2.90
604 706 5.702865 CAATGGTAACTTGTGTTGAGATGG 58.297 41.667 0.00 0.00 37.59 3.51
605 707 4.431416 TGGTAACTTGTGTTGAGATGGT 57.569 40.909 0.00 0.00 37.59 3.55
606 708 4.133820 TGGTAACTTGTGTTGAGATGGTG 58.866 43.478 0.00 0.00 37.59 4.17
607 709 3.058224 GGTAACTTGTGTTGAGATGGTGC 60.058 47.826 0.00 0.00 37.59 5.01
608 710 1.609208 ACTTGTGTTGAGATGGTGCC 58.391 50.000 0.00 0.00 0.00 5.01
609 711 0.518636 CTTGTGTTGAGATGGTGCCG 59.481 55.000 0.00 0.00 0.00 5.69
610 712 0.107643 TTGTGTTGAGATGGTGCCGA 59.892 50.000 0.00 0.00 0.00 5.54
611 713 0.324614 TGTGTTGAGATGGTGCCGAT 59.675 50.000 0.00 0.00 0.00 4.18
612 714 0.729116 GTGTTGAGATGGTGCCGATG 59.271 55.000 0.00 0.00 0.00 3.84
613 715 0.612744 TGTTGAGATGGTGCCGATGA 59.387 50.000 0.00 0.00 0.00 2.92
620 722 2.437281 AGATGGTGCCGATGAATCTTCT 59.563 45.455 0.00 0.00 0.00 2.85
636 738 1.898472 CTTCTGAGACAAGAGGGAGCA 59.102 52.381 0.00 0.00 0.00 4.26
718 820 2.189257 TGTGCCTTGTGCTCACGT 59.811 55.556 0.00 0.00 38.48 4.49
839 949 3.023832 CTGACCCAACAAGAAAACCAGT 58.976 45.455 0.00 0.00 0.00 4.00
889 1035 3.167945 CCGTTGGACGTACGTCGC 61.168 66.667 34.69 27.98 45.41 5.19
891 1037 2.127270 GTTGGACGTACGTCGCGA 60.127 61.111 34.69 25.54 45.41 5.87
897 1043 3.517699 CGTACGTCGCGACCAACG 61.518 66.667 32.58 32.58 44.22 4.10
940 1088 0.525311 CATGGCCAATTACGTGTGCA 59.475 50.000 10.96 0.00 0.00 4.57
945 1093 1.468520 GCCAATTACGTGTGCATCACT 59.531 47.619 14.60 7.03 44.16 3.41
953 1107 1.737029 CGTGTGCATCACTAGGTCCTG 60.737 57.143 0.00 0.00 44.16 3.86
975 1129 6.003859 TGGAAAAACCGGCCTATAAATCTA 57.996 37.500 0.00 0.00 42.61 1.98
988 1142 1.871080 AAATCTATCTTGGCGCCTCG 58.129 50.000 29.70 18.38 0.00 4.63
991 1145 1.300233 CTATCTTGGCGCCTCGTCC 60.300 63.158 29.70 0.00 0.00 4.79
994 1148 3.458163 CTTGGCGCCTCGTCCCTA 61.458 66.667 29.70 0.07 0.00 3.53
995 1149 3.718210 CTTGGCGCCTCGTCCCTAC 62.718 68.421 29.70 0.00 0.00 3.18
1008 1162 2.297597 CGTCCCTACCCATCTCATTCTC 59.702 54.545 0.00 0.00 0.00 2.87
1016 1172 2.885266 CCCATCTCATTCTCATTGCCTG 59.115 50.000 0.00 0.00 0.00 4.85
1020 1176 1.938577 CTCATTCTCATTGCCTGGACG 59.061 52.381 0.00 0.00 0.00 4.79
1021 1177 0.379669 CATTCTCATTGCCTGGACGC 59.620 55.000 0.00 0.00 0.00 5.19
1022 1178 0.254178 ATTCTCATTGCCTGGACGCT 59.746 50.000 0.00 0.00 0.00 5.07
1023 1179 0.674581 TTCTCATTGCCTGGACGCTG 60.675 55.000 0.00 0.00 0.00 5.18
1024 1180 2.046023 TCATTGCCTGGACGCTGG 60.046 61.111 0.00 0.00 0.00 4.85
1025 1181 2.046023 CATTGCCTGGACGCTGGA 60.046 61.111 0.00 0.00 0.00 3.86
1026 1182 1.452651 CATTGCCTGGACGCTGGAT 60.453 57.895 0.00 0.00 0.00 3.41
1027 1183 1.033746 CATTGCCTGGACGCTGGATT 61.034 55.000 0.00 0.00 0.00 3.01
1028 1184 0.546122 ATTGCCTGGACGCTGGATTA 59.454 50.000 0.00 0.00 0.00 1.75
1029 1185 0.326595 TTGCCTGGACGCTGGATTAA 59.673 50.000 0.00 0.00 0.00 1.40
1030 1186 0.326595 TGCCTGGACGCTGGATTAAA 59.673 50.000 0.00 0.00 0.00 1.52
1031 1187 0.733150 GCCTGGACGCTGGATTAAAC 59.267 55.000 0.00 0.00 0.00 2.01
1032 1188 1.948611 GCCTGGACGCTGGATTAAACA 60.949 52.381 0.00 0.00 0.00 2.83
1033 1189 2.009774 CCTGGACGCTGGATTAAACAG 58.990 52.381 6.25 6.25 38.95 3.16
1034 1190 2.009774 CTGGACGCTGGATTAAACAGG 58.990 52.381 11.19 5.53 36.48 4.00
1035 1191 1.349688 TGGACGCTGGATTAAACAGGT 59.650 47.619 11.19 7.94 36.48 4.00
1036 1192 2.568062 TGGACGCTGGATTAAACAGGTA 59.432 45.455 11.19 0.00 36.48 3.08
1037 1193 3.195661 GGACGCTGGATTAAACAGGTAG 58.804 50.000 11.19 0.00 36.48 3.18
1038 1194 2.608090 GACGCTGGATTAAACAGGTAGC 59.392 50.000 11.19 0.00 36.48 3.58
1039 1195 2.236395 ACGCTGGATTAAACAGGTAGCT 59.764 45.455 11.19 0.00 36.48 3.32
1040 1196 3.449737 ACGCTGGATTAAACAGGTAGCTA 59.550 43.478 11.19 0.00 36.48 3.32
1041 1197 4.051922 CGCTGGATTAAACAGGTAGCTAG 58.948 47.826 11.19 0.00 36.48 3.42
1042 1198 4.381411 GCTGGATTAAACAGGTAGCTAGG 58.619 47.826 11.19 0.00 36.48 3.02
1043 1199 4.381411 CTGGATTAAACAGGTAGCTAGGC 58.619 47.826 0.00 0.00 32.38 3.93
1050 1206 0.460284 CAGGTAGCTAGGCAACACCG 60.460 60.000 0.00 0.00 46.52 4.94
1069 1225 3.411351 CGCGTACGGCAGCTTGTT 61.411 61.111 18.39 0.00 43.84 2.83
1070 1226 2.173382 GCGTACGGCAGCTTGTTG 59.827 61.111 18.39 0.00 42.87 3.33
1071 1227 2.314647 GCGTACGGCAGCTTGTTGA 61.315 57.895 18.39 0.00 42.87 3.18
1087 1243 1.256635 GTTGAAGCTTAGCTCGATCGC 59.743 52.381 11.09 0.00 38.25 4.58
1099 1255 2.879462 GATCGCGTGTGTCCGTCC 60.879 66.667 5.77 0.00 0.00 4.79
1326 1482 2.284921 CCACCAGCCTCCTCCTCA 60.285 66.667 0.00 0.00 0.00 3.86
1327 1483 2.365586 CCACCAGCCTCCTCCTCAG 61.366 68.421 0.00 0.00 0.00 3.35
1328 1484 2.686835 ACCAGCCTCCTCCTCAGC 60.687 66.667 0.00 0.00 0.00 4.26
1329 1485 3.478274 CCAGCCTCCTCCTCAGCC 61.478 72.222 0.00 0.00 0.00 4.85
1357 1513 3.993614 AATGCCGCTTCCGCATCCA 62.994 57.895 0.00 0.00 32.71 3.41
1369 1525 3.445687 CATCCACCCCGACGACGA 61.446 66.667 9.28 0.00 42.66 4.20
1370 1526 2.677524 ATCCACCCCGACGACGAA 60.678 61.111 9.28 0.00 42.66 3.85
1371 1527 2.998279 ATCCACCCCGACGACGAAC 61.998 63.158 9.28 0.00 42.66 3.95
1427 1583 0.859232 CGGACGTCCTCAACAAAGTG 59.141 55.000 30.92 8.65 0.00 3.16
1456 1612 2.816718 GGCCACGCCTATCGGTAA 59.183 61.111 0.00 0.00 46.69 2.85
1460 1616 0.874607 CCACGCCTATCGGTAAGCAC 60.875 60.000 0.00 0.00 43.86 4.40
1468 1624 3.487202 CGGTAAGCACGCACGCAT 61.487 61.111 0.00 0.00 0.00 4.73
1469 1625 2.162120 CGGTAAGCACGCACGCATA 61.162 57.895 0.00 0.00 0.00 3.14
1489 1762 1.080298 CGCGTGGCACCATTAGTTTA 58.920 50.000 12.86 0.00 0.00 2.01
1496 1769 5.193679 GTGGCACCATTAGTTTAGAGGAAT 58.806 41.667 6.29 0.00 0.00 3.01
1497 1770 5.066505 GTGGCACCATTAGTTTAGAGGAATG 59.933 44.000 6.29 0.00 0.00 2.67
1504 1777 3.402628 AGTTTAGAGGAATGTGCACGT 57.597 42.857 13.13 9.52 0.00 4.49
1505 1778 3.740115 AGTTTAGAGGAATGTGCACGTT 58.260 40.909 23.99 23.99 0.00 3.99
1506 1779 4.134563 AGTTTAGAGGAATGTGCACGTTT 58.865 39.130 24.49 14.63 0.00 3.60
1507 1780 4.213482 AGTTTAGAGGAATGTGCACGTTTC 59.787 41.667 24.49 22.56 0.00 2.78
1512 1785 2.293399 AGGAATGTGCACGTTTCTTTCC 59.707 45.455 24.40 19.92 36.38 3.13
1522 1795 2.288729 ACGTTTCTTTCCTGGCGTTAAC 59.711 45.455 0.00 0.00 0.00 2.01
1530 1803 1.210722 TCCTGGCGTTAACCATGCATA 59.789 47.619 0.00 0.00 39.54 3.14
1531 1804 2.158682 TCCTGGCGTTAACCATGCATAT 60.159 45.455 0.00 0.00 39.54 1.78
1543 1816 2.733552 CCATGCATATGTACGCTCTGAC 59.266 50.000 0.00 0.00 32.21 3.51
1546 1819 4.123497 TGCATATGTACGCTCTGACTTT 57.877 40.909 4.29 0.00 0.00 2.66
1592 1865 1.337703 CGGATCAGAGGAGAAGCAGAG 59.662 57.143 0.00 0.00 0.00 3.35
1620 1893 1.803519 GGAGCTGCACGACGAAGAG 60.804 63.158 0.00 0.00 0.00 2.85
1678 1951 3.720106 CTCGTCGTCGGCTTCCTCG 62.720 68.421 1.55 0.00 37.69 4.63
1910 2183 1.517257 CGTACAAGCTCGGCCTCAG 60.517 63.158 0.00 0.00 0.00 3.35
2026 2299 2.126071 ACGGCAACCACGAGATCG 60.126 61.111 0.00 0.00 46.33 3.69
2043 2316 2.185608 GCGCTCCTGGACTTCCTC 59.814 66.667 0.00 0.00 36.82 3.71
2298 2571 1.743252 CGAGGAGCAGAACAAGCCC 60.743 63.158 0.00 0.00 0.00 5.19
2507 2780 2.737376 GAGGCGGTTCCACGACAC 60.737 66.667 0.00 0.00 46.48 3.67
2601 2874 3.372730 GCCATTGTTGCCGCCAGA 61.373 61.111 0.00 0.00 0.00 3.86
2605 2878 0.597568 CATTGTTGCCGCCAGAAGAA 59.402 50.000 0.00 0.00 0.00 2.52
2615 2888 1.201429 GCCAGAAGAAGGGGGTGAGA 61.201 60.000 0.00 0.00 0.00 3.27
2641 2927 1.523711 CGGCCCGTGCAAGACATAT 60.524 57.895 0.00 0.00 40.13 1.78
2645 2935 0.378257 CCCGTGCAAGACATATGTGC 59.622 55.000 14.43 11.38 38.78 4.57
2653 2943 5.184711 TGCAAGACATATGTGCACTCATTA 58.815 37.500 19.41 5.21 43.09 1.90
2669 2959 6.200286 GCACTCATTAATTCATTGCTGATTGG 59.800 38.462 0.00 0.00 0.00 3.16
2672 2962 7.558807 ACTCATTAATTCATTGCTGATTGGAGA 59.441 33.333 0.00 0.00 0.00 3.71
2675 2965 8.978539 CATTAATTCATTGCTGATTGGAGATTG 58.021 33.333 0.00 0.00 0.00 2.67
2828 3129 4.304110 CATGATAGTCCATGCAATTTGGC 58.696 43.478 0.00 0.00 37.68 4.52
2832 3133 0.669932 GTCCATGCAATTTGGCGCAA 60.670 50.000 10.83 0.00 42.37 4.85
2988 3290 2.683968 TCACACATGTAGCGAAGGAAC 58.316 47.619 0.00 0.00 0.00 3.62
3035 3340 0.612174 CAGAGGAGGGAGTCGGTTGA 60.612 60.000 0.00 0.00 0.00 3.18
3122 3427 1.414158 ACTGCCGTGGTATGCTATCT 58.586 50.000 0.00 0.00 0.00 1.98
3200 3506 3.735237 TTTCTCTCTGAGTCGCACTTT 57.265 42.857 4.32 0.00 0.00 2.66
3210 3516 7.602644 TCTCTGAGTCGCACTTTAATAAATGTT 59.397 33.333 4.32 0.00 0.00 2.71
3300 3607 4.007659 CGGTGGCCTAGTTTTGTTCTATT 58.992 43.478 3.32 0.00 0.00 1.73
3411 3723 1.745827 CGGGCTTTTATGGTCATCCGT 60.746 52.381 0.00 0.00 36.30 4.69
3435 3747 4.689612 TGGAGTGAGCATAGTTTATCCC 57.310 45.455 0.00 0.00 0.00 3.85
3491 3803 1.457165 CCCGTGGGTGGTTTTAGGT 59.543 57.895 0.00 0.00 0.00 3.08
3575 3887 3.065786 TGATGAGAGATTTCCGCAATTGC 59.934 43.478 20.76 20.76 37.78 3.56
3639 3953 1.627834 CTTTCACTTGGAGGAGAGGCT 59.372 52.381 0.00 0.00 0.00 4.58
3641 3955 2.151502 TCACTTGGAGGAGAGGCTAG 57.848 55.000 0.00 0.00 0.00 3.42
3703 4017 0.107361 GCGAATATATTCCCCCGGGG 60.107 60.000 34.65 34.65 46.11 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.375174 ACACATAAAGGGTGAGGCAAGA 59.625 45.455 0.00 0.00 39.53 3.02
13 14 6.532302 GGCCGTATTTTAAAACACATAAAGGG 59.468 38.462 9.84 2.91 0.00 3.95
16 17 7.229581 AGGGCCGTATTTTAAAACACATAAA 57.770 32.000 9.84 0.00 0.00 1.40
34 36 3.074412 GGTAAATGATGTGATAGGGCCG 58.926 50.000 0.00 0.00 0.00 6.13
85 89 9.438228 GAGATCAATGATGTGACTTGATGATAT 57.562 33.333 0.00 0.00 39.16 1.63
86 90 8.426489 TGAGATCAATGATGTGACTTGATGATA 58.574 33.333 0.00 0.00 39.16 2.15
91 95 6.704310 TCTTGAGATCAATGATGTGACTTGA 58.296 36.000 0.00 0.00 35.02 3.02
182 186 3.388024 AGTGCACTCTTGTTCAAGGTAGA 59.612 43.478 15.25 0.00 0.00 2.59
183 187 3.733337 AGTGCACTCTTGTTCAAGGTAG 58.267 45.455 15.25 6.29 0.00 3.18
184 188 3.838244 AGTGCACTCTTGTTCAAGGTA 57.162 42.857 15.25 0.00 0.00 3.08
215 220 6.790461 TGAGGCCCTAAATACTATTCACCATA 59.210 38.462 0.00 0.00 0.00 2.74
248 253 7.016661 GGATATATATTATGGAGGGAGTGGTGG 59.983 44.444 0.00 0.00 0.00 4.61
289 296 3.056607 CCCATCATCTCCCACAAACAAAC 60.057 47.826 0.00 0.00 0.00 2.93
295 302 2.378208 TCAAACCCATCATCTCCCACAA 59.622 45.455 0.00 0.00 0.00 3.33
411 418 3.191371 CCCTGATACCAAAAGTGCAAGAC 59.809 47.826 0.00 0.00 0.00 3.01
483 490 7.420214 GGGGTCTCAAGAAACTATTGGATGATA 60.420 40.741 0.00 0.00 0.00 2.15
496 503 4.177537 TGTGAAATGGGGTCTCAAGAAA 57.822 40.909 0.00 0.00 0.00 2.52
506 513 3.689347 TCTGTGATCTTGTGAAATGGGG 58.311 45.455 0.00 0.00 0.00 4.96
523 530 7.014615 AGCAAAGGTTTCTATCAACATTTCTGT 59.985 33.333 0.00 0.00 38.30 3.41
542 549 1.928503 CAACAACAACAGCAGCAAAGG 59.071 47.619 0.00 0.00 0.00 3.11
547 554 0.098728 ACGACAACAACAACAGCAGC 59.901 50.000 0.00 0.00 0.00 5.25
549 556 0.371989 CGACGACAACAACAACAGCA 59.628 50.000 0.00 0.00 0.00 4.41
550 557 0.372334 ACGACGACAACAACAACAGC 59.628 50.000 0.00 0.00 0.00 4.40
551 558 1.330818 CGACGACGACAACAACAACAG 60.331 52.381 0.00 0.00 42.66 3.16
578 680 3.291584 TCAACACAAGTTACCATTGCCA 58.708 40.909 0.00 0.00 35.85 4.92
579 681 3.568007 TCTCAACACAAGTTACCATTGCC 59.432 43.478 0.00 0.00 35.85 4.52
580 682 4.829064 TCTCAACACAAGTTACCATTGC 57.171 40.909 0.00 0.00 35.85 3.56
581 683 5.241506 ACCATCTCAACACAAGTTACCATTG 59.758 40.000 0.00 0.00 35.85 2.82
582 684 5.241506 CACCATCTCAACACAAGTTACCATT 59.758 40.000 0.00 0.00 35.85 3.16
583 685 4.761739 CACCATCTCAACACAAGTTACCAT 59.238 41.667 0.00 0.00 35.85 3.55
584 686 4.133820 CACCATCTCAACACAAGTTACCA 58.866 43.478 0.00 0.00 35.85 3.25
585 687 3.058224 GCACCATCTCAACACAAGTTACC 60.058 47.826 0.00 0.00 35.85 2.85
586 688 3.058224 GGCACCATCTCAACACAAGTTAC 60.058 47.826 0.00 0.00 35.85 2.50
587 689 3.146066 GGCACCATCTCAACACAAGTTA 58.854 45.455 0.00 0.00 35.85 2.24
588 690 1.956477 GGCACCATCTCAACACAAGTT 59.044 47.619 0.00 0.00 38.88 2.66
589 691 1.609208 GGCACCATCTCAACACAAGT 58.391 50.000 0.00 0.00 0.00 3.16
590 692 0.518636 CGGCACCATCTCAACACAAG 59.481 55.000 0.00 0.00 0.00 3.16
591 693 0.107643 TCGGCACCATCTCAACACAA 59.892 50.000 0.00 0.00 0.00 3.33
592 694 0.324614 ATCGGCACCATCTCAACACA 59.675 50.000 0.00 0.00 0.00 3.72
593 695 0.729116 CATCGGCACCATCTCAACAC 59.271 55.000 0.00 0.00 0.00 3.32
594 696 0.612744 TCATCGGCACCATCTCAACA 59.387 50.000 0.00 0.00 0.00 3.33
595 697 1.737838 TTCATCGGCACCATCTCAAC 58.262 50.000 0.00 0.00 0.00 3.18
596 698 2.171237 AGATTCATCGGCACCATCTCAA 59.829 45.455 0.00 0.00 0.00 3.02
597 699 1.764723 AGATTCATCGGCACCATCTCA 59.235 47.619 0.00 0.00 0.00 3.27
598 700 2.540265 AGATTCATCGGCACCATCTC 57.460 50.000 0.00 0.00 0.00 2.75
599 701 2.437281 AGAAGATTCATCGGCACCATCT 59.563 45.455 0.00 0.00 0.00 2.90
600 702 2.547211 CAGAAGATTCATCGGCACCATC 59.453 50.000 0.00 0.00 0.00 3.51
601 703 2.171237 TCAGAAGATTCATCGGCACCAT 59.829 45.455 0.00 0.00 0.00 3.55
602 704 1.554617 TCAGAAGATTCATCGGCACCA 59.445 47.619 0.00 0.00 0.00 4.17
603 705 2.159043 TCTCAGAAGATTCATCGGCACC 60.159 50.000 0.00 0.00 0.00 5.01
604 706 2.863137 GTCTCAGAAGATTCATCGGCAC 59.137 50.000 0.00 0.00 33.08 5.01
605 707 2.497273 TGTCTCAGAAGATTCATCGGCA 59.503 45.455 0.00 0.00 33.08 5.69
606 708 3.170791 TGTCTCAGAAGATTCATCGGC 57.829 47.619 0.00 0.00 33.08 5.54
607 709 5.003692 TCTTGTCTCAGAAGATTCATCGG 57.996 43.478 0.00 0.00 33.08 4.18
608 710 5.042593 CCTCTTGTCTCAGAAGATTCATCG 58.957 45.833 0.00 0.00 33.08 3.84
609 711 5.128499 TCCCTCTTGTCTCAGAAGATTCATC 59.872 44.000 0.00 0.00 33.08 2.92
610 712 5.028802 TCCCTCTTGTCTCAGAAGATTCAT 58.971 41.667 0.00 0.00 33.08 2.57
611 713 4.420206 TCCCTCTTGTCTCAGAAGATTCA 58.580 43.478 0.00 0.00 33.08 2.57
612 714 4.680440 GCTCCCTCTTGTCTCAGAAGATTC 60.680 50.000 0.00 0.00 33.08 2.52
613 715 3.197549 GCTCCCTCTTGTCTCAGAAGATT 59.802 47.826 0.00 0.00 33.08 2.40
620 722 2.290514 CCATTTGCTCCCTCTTGTCTCA 60.291 50.000 0.00 0.00 0.00 3.27
636 738 0.608035 ACGACGCCATTGGTCCATTT 60.608 50.000 4.26 0.00 0.00 2.32
718 820 3.234630 CTTCAAGCCCGACCGTGGA 62.235 63.158 0.00 0.00 0.00 4.02
757 859 2.118076 TTTGCAGGGCAGGAAGGG 59.882 61.111 0.00 0.00 40.61 3.95
812 922 0.690762 TCTTGTTGGGTCAGGCCTAC 59.309 55.000 3.98 4.21 37.43 3.18
839 949 2.811410 ACCTAGTTGACATGACCCGTA 58.189 47.619 0.00 0.00 0.00 4.02
891 1037 1.607251 GGACAAGGAATCGACGTTGGT 60.607 52.381 2.20 0.00 39.12 3.67
897 1043 1.814169 GCGGGGACAAGGAATCGAC 60.814 63.158 0.00 0.00 0.00 4.20
940 1088 3.307480 CGGTTTTTCCAGGACCTAGTGAT 60.307 47.826 0.00 0.00 35.57 3.06
945 1093 0.037160 GCCGGTTTTTCCAGGACCTA 59.963 55.000 1.90 0.00 35.57 3.08
953 1107 6.940867 AGATAGATTTATAGGCCGGTTTTTCC 59.059 38.462 1.90 0.00 0.00 3.13
975 1129 4.162690 GGGACGAGGCGCCAAGAT 62.163 66.667 31.54 7.63 0.00 2.40
988 1142 3.309296 TGAGAATGAGATGGGTAGGGAC 58.691 50.000 0.00 0.00 0.00 4.46
991 1145 4.070716 GCAATGAGAATGAGATGGGTAGG 58.929 47.826 0.00 0.00 0.00 3.18
994 1148 2.512896 AGGCAATGAGAATGAGATGGGT 59.487 45.455 0.00 0.00 0.00 4.51
995 1149 2.885266 CAGGCAATGAGAATGAGATGGG 59.115 50.000 0.00 0.00 0.00 4.00
1008 1162 1.033746 AATCCAGCGTCCAGGCAATG 61.034 55.000 0.00 0.00 34.64 2.82
1016 1172 2.109425 ACCTGTTTAATCCAGCGTCC 57.891 50.000 0.00 0.00 0.00 4.79
1020 1176 4.381411 CCTAGCTACCTGTTTAATCCAGC 58.619 47.826 0.00 0.00 0.00 4.85
1021 1177 4.141711 TGCCTAGCTACCTGTTTAATCCAG 60.142 45.833 0.00 0.00 0.00 3.86
1022 1178 3.778075 TGCCTAGCTACCTGTTTAATCCA 59.222 43.478 0.00 0.00 0.00 3.41
1023 1179 4.417426 TGCCTAGCTACCTGTTTAATCC 57.583 45.455 0.00 0.00 0.00 3.01
1024 1180 5.064834 GTGTTGCCTAGCTACCTGTTTAATC 59.935 44.000 0.00 0.00 33.72 1.75
1025 1181 4.941873 GTGTTGCCTAGCTACCTGTTTAAT 59.058 41.667 0.00 0.00 33.72 1.40
1026 1182 4.320870 GTGTTGCCTAGCTACCTGTTTAA 58.679 43.478 0.00 0.00 33.72 1.52
1027 1183 3.307199 GGTGTTGCCTAGCTACCTGTTTA 60.307 47.826 0.00 0.00 33.72 2.01
1028 1184 2.552373 GGTGTTGCCTAGCTACCTGTTT 60.552 50.000 0.00 0.00 33.72 2.83
1029 1185 1.003233 GGTGTTGCCTAGCTACCTGTT 59.997 52.381 0.00 0.00 33.72 3.16
1030 1186 0.613777 GGTGTTGCCTAGCTACCTGT 59.386 55.000 0.00 0.00 33.72 4.00
1031 1187 0.460284 CGGTGTTGCCTAGCTACCTG 60.460 60.000 0.00 0.00 33.72 4.00
1032 1188 1.614241 CCGGTGTTGCCTAGCTACCT 61.614 60.000 0.00 0.00 33.72 3.08
1033 1189 1.153429 CCGGTGTTGCCTAGCTACC 60.153 63.158 0.00 0.00 33.72 3.18
1034 1190 1.814169 GCCGGTGTTGCCTAGCTAC 60.814 63.158 1.90 0.00 35.10 3.58
1035 1191 2.582436 GCCGGTGTTGCCTAGCTA 59.418 61.111 1.90 0.00 33.11 3.32
1036 1192 4.760047 CGCCGGTGTTGCCTAGCT 62.760 66.667 6.91 0.00 33.54 3.32
1064 1220 3.000277 CGATCGAGCTAAGCTTCAACAAG 60.000 47.826 10.26 0.00 39.88 3.16
1065 1221 2.923655 CGATCGAGCTAAGCTTCAACAA 59.076 45.455 10.26 0.00 39.88 2.83
1066 1222 2.530177 CGATCGAGCTAAGCTTCAACA 58.470 47.619 10.26 0.00 39.88 3.33
1067 1223 1.256635 GCGATCGAGCTAAGCTTCAAC 59.743 52.381 21.57 0.00 39.88 3.18
1068 1224 1.560923 GCGATCGAGCTAAGCTTCAA 58.439 50.000 21.57 0.00 39.88 2.69
1069 1225 0.592500 CGCGATCGAGCTAAGCTTCA 60.593 55.000 21.57 0.00 39.88 3.02
1070 1226 0.592754 ACGCGATCGAGCTAAGCTTC 60.593 55.000 21.57 0.00 39.88 3.86
1071 1227 0.867753 CACGCGATCGAGCTAAGCTT 60.868 55.000 21.57 3.48 39.88 3.74
1078 1234 3.248171 GGACACACGCGATCGAGC 61.248 66.667 21.57 0.00 39.41 5.03
1087 1243 3.277211 ATGGACGGACGGACACACG 62.277 63.158 0.00 0.00 40.31 4.49
1120 1276 4.899239 CCGCCGACTCCAGCATCC 62.899 72.222 0.00 0.00 0.00 3.51
1414 1570 0.534203 GCCCGACACTTTGTTGAGGA 60.534 55.000 0.00 0.00 33.58 3.71
1451 1607 2.162120 TATGCGTGCGTGCTTACCG 61.162 57.895 0.00 0.00 35.36 4.02
1468 1624 0.037139 AACTAATGGTGCCACGCGTA 60.037 50.000 13.44 0.00 0.00 4.42
1469 1625 0.887387 AAACTAATGGTGCCACGCGT 60.887 50.000 5.58 5.58 0.00 6.01
1473 1629 4.216411 TCCTCTAAACTAATGGTGCCAC 57.784 45.455 0.00 0.00 0.00 5.01
1481 1637 5.488341 ACGTGCACATTCCTCTAAACTAAT 58.512 37.500 18.64 0.00 0.00 1.73
1489 1762 2.550830 AGAAACGTGCACATTCCTCT 57.449 45.000 22.10 10.54 0.00 3.69
1496 1769 1.021202 CCAGGAAAGAAACGTGCACA 58.979 50.000 18.64 0.00 0.00 4.57
1497 1770 0.317854 GCCAGGAAAGAAACGTGCAC 60.318 55.000 6.82 6.82 0.00 4.57
1504 1777 2.933573 TGGTTAACGCCAGGAAAGAAA 58.066 42.857 0.00 0.00 33.97 2.52
1505 1778 2.642154 TGGTTAACGCCAGGAAAGAA 57.358 45.000 0.00 0.00 33.97 2.52
1506 1779 2.432444 CATGGTTAACGCCAGGAAAGA 58.568 47.619 0.00 0.00 42.37 2.52
1507 1780 1.135402 GCATGGTTAACGCCAGGAAAG 60.135 52.381 1.27 0.00 42.37 2.62
1512 1785 2.618241 ACATATGCATGGTTAACGCCAG 59.382 45.455 10.16 0.00 42.47 4.85
1522 1795 2.733552 GTCAGAGCGTACATATGCATGG 59.266 50.000 10.16 3.88 40.60 3.66
1530 1803 3.522553 GGCTAAAAGTCAGAGCGTACAT 58.477 45.455 0.00 0.00 37.07 2.29
1531 1804 2.670229 CGGCTAAAAGTCAGAGCGTACA 60.670 50.000 0.00 0.00 37.07 2.90
1572 1845 1.337703 CTCTGCTTCTCCTCTGATCCG 59.662 57.143 0.00 0.00 0.00 4.18
1620 1893 1.061485 GCTTGTCGTCCGACTCTTTC 58.939 55.000 19.30 2.82 44.80 2.62
1883 2156 1.654954 GAGCTTGTACGCCTCGAGGA 61.655 60.000 35.69 11.93 37.39 3.71
1892 2165 1.517257 CTGAGGCCGAGCTTGTACG 60.517 63.158 0.00 0.00 0.00 3.67
1906 2179 2.045536 GAAGGTGGCTGGGCTGAG 60.046 66.667 0.00 0.00 0.00 3.35
1910 2183 2.747855 CGAAGAAGGTGGCTGGGC 60.748 66.667 0.00 0.00 0.00 5.36
1914 2187 1.289380 GTCGTCGAAGAAGGTGGCT 59.711 57.895 1.62 0.00 39.69 4.75
2026 2299 2.185608 GAGGAAGTCCAGGAGCGC 59.814 66.667 0.00 0.00 38.89 5.92
2298 2571 2.523184 TCTGGAAGTAGCGCGTCACG 62.523 60.000 8.43 0.00 39.43 4.35
2454 2727 1.428370 CGTCCATGGCCATGTACACG 61.428 60.000 37.30 33.91 37.11 4.49
2601 2874 0.405973 GGCTTTCTCACCCCCTTCTT 59.594 55.000 0.00 0.00 0.00 2.52
2605 2878 1.460699 GTTGGCTTTCTCACCCCCT 59.539 57.895 0.00 0.00 0.00 4.79
2634 2920 8.687292 ATGAATTAATGAGTGCACATATGTCT 57.313 30.769 21.04 0.00 0.00 3.41
2641 2927 5.183522 TCAGCAATGAATTAATGAGTGCACA 59.816 36.000 21.04 0.00 32.98 4.57
2645 2935 7.485810 TCCAATCAGCAATGAATTAATGAGTG 58.514 34.615 8.81 8.81 33.27 3.51
2647 2937 7.937649 TCTCCAATCAGCAATGAATTAATGAG 58.062 34.615 0.00 0.00 0.00 2.90
2653 2943 6.540438 ACAATCTCCAATCAGCAATGAATT 57.460 33.333 0.00 0.00 0.00 2.17
2836 3137 5.127031 ACATTACAATTACAGGGATTGGCAC 59.873 40.000 0.00 0.00 38.50 5.01
2846 3147 5.364778 TGATCCGGGACATTACAATTACAG 58.635 41.667 0.00 0.00 0.00 2.74
2988 3290 1.254284 ACGCCTCCTCTTCCTCTGTG 61.254 60.000 0.00 0.00 0.00 3.66
3035 3340 2.256591 GCCGATGCGCCATCATCTT 61.257 57.895 4.18 0.00 40.54 2.40
3122 3427 3.664025 CTCGCGAACTGCCATGGGA 62.664 63.158 15.13 10.50 42.08 4.37
3200 3506 7.414436 GCAACTCATCGGCTTAACATTTATTA 58.586 34.615 0.00 0.00 0.00 0.98
3210 3516 0.800683 CGACGCAACTCATCGGCTTA 60.801 55.000 0.00 0.00 32.22 3.09
3259 3566 4.227134 CCCGGCCATCACTCTCCG 62.227 72.222 2.24 0.00 41.41 4.63
3368 3677 2.023181 CGCCAATGCACGGAATCG 59.977 61.111 8.20 0.00 43.02 3.34
3411 3723 5.885912 GGGATAAACTATGCTCACTCCAAAA 59.114 40.000 0.00 0.00 0.00 2.44
3435 3747 0.464452 AGGTTTCGGAGCTTATCCCG 59.536 55.000 5.25 5.25 46.50 5.14
3575 3887 1.439644 GAGGCCGCACTCTCCTAAG 59.560 63.158 0.00 0.00 34.65 2.18
3639 3953 6.353323 CCATGTCAAGTCTCTCTCTAGTCTA 58.647 44.000 0.00 0.00 0.00 2.59
3641 3955 4.202010 GCCATGTCAAGTCTCTCTCTAGTC 60.202 50.000 0.00 0.00 0.00 2.59
3703 4017 5.065988 ACATGTTCCTCATTTATAACCGCAC 59.934 40.000 0.00 0.00 34.09 5.34
3741 4061 3.648067 TCAGTATCCAAGATGATGGGACC 59.352 47.826 0.00 0.00 41.05 4.46


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

AutoCloner maintained by Alex Coulton.