Multiple sequence alignment - TraesCS5A01G461200

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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 TraesCS5A01G461200 chr5A 100.000 2804 0 0 1 2804 641675026 641677829 0.000000e+00 5179.0
1 TraesCS5A01G461200 chr5A 93.767 738 44 1 1 738 359037300 359036565 0.000000e+00 1107.0
2 TraesCS5A01G461200 chr5A 95.290 276 11 2 6 280 563374922 563374648 1.190000e-118 436.0
3 TraesCS5A01G461200 chr5A 93.191 235 12 1 512 746 563372477 563372247 2.670000e-90 342.0
4 TraesCS5A01G461200 chr5A 93.194 191 12 1 272 462 563372664 563372475 2.130000e-71 279.0
5 TraesCS5A01G461200 chr5A 89.474 95 4 1 748 842 59713491 59713403 6.350000e-22 115.0
6 TraesCS5A01G461200 chr7A 93.080 737 51 0 11 747 57088216 57088952 0.000000e+00 1079.0
7 TraesCS5A01G461200 chr7A 95.283 106 3 2 742 845 693395553 693395658 1.730000e-37 167.0
8 TraesCS5A01G461200 chr7A 77.249 189 40 2 1738 1923 158407666 158407854 1.060000e-19 108.0
9 TraesCS5A01G461200 chr7A 76.098 205 32 12 1736 1930 535929737 535929934 1.070000e-14 91.6
10 TraesCS5A01G461200 chr5B 87.486 871 54 30 849 1710 644854335 644855159 0.000000e+00 953.0
11 TraesCS5A01G461200 chr5B 88.997 618 63 3 1761 2377 644856405 644857018 0.000000e+00 760.0
12 TraesCS5A01G461200 chr5B 85.940 569 63 11 2239 2802 644857020 644857576 2.410000e-165 592.0
13 TraesCS5A01G461200 chr5B 87.770 278 21 6 849 1126 644852872 644853136 2.100000e-81 313.0
14 TraesCS5A01G461200 chr5D 91.071 672 35 7 844 1514 513893800 513894447 0.000000e+00 885.0
15 TraesCS5A01G461200 chr5D 88.186 711 79 2 1709 2418 513896731 513897437 0.000000e+00 843.0
16 TraesCS5A01G461200 chr5D 91.365 498 37 3 844 1341 513884799 513885290 0.000000e+00 676.0
17 TraesCS5A01G461200 chr5D 87.565 386 31 11 2421 2804 513899660 513900030 5.550000e-117 431.0
18 TraesCS5A01G461200 chr5D 95.714 70 2 1 1641 1710 513894528 513894596 8.210000e-21 111.0
19 TraesCS5A01G461200 chr7B 92.644 435 29 3 316 749 626055359 626054927 8.530000e-175 623.0
20 TraesCS5A01G461200 chr7B 80.973 226 36 5 1713 1932 100004866 100004642 3.710000e-39 172.0
21 TraesCS5A01G461200 chr3B 89.493 276 29 0 63 338 557614365 557614640 1.600000e-92 350.0
22 TraesCS5A01G461200 chr3B 83.884 242 26 6 515 753 557621595 557621826 4.700000e-53 219.0
23 TraesCS5A01G461200 chr2D 90.000 220 20 2 25 244 18753771 18753554 1.640000e-72 283.0
24 TraesCS5A01G461200 chr2D 90.323 93 4 2 748 840 309942537 309942450 1.760000e-22 117.0
25 TraesCS5A01G461200 chr3A 94.059 101 5 1 745 844 572529464 572529364 4.840000e-33 152.0
26 TraesCS5A01G461200 chr2A 94.898 98 4 1 745 842 239412876 239412780 4.840000e-33 152.0
27 TraesCS5A01G461200 chr6A 93.939 99 5 1 742 839 359016379 359016477 6.260000e-32 148.0
28 TraesCS5A01G461200 chr6A 77.720 193 36 7 1718 1905 614540030 614539840 8.210000e-21 111.0
29 TraesCS5A01G461200 chr4D 78.667 225 44 4 1709 1930 44051446 44051669 2.250000e-31 147.0
30 TraesCS5A01G461200 chr2B 78.894 199 28 5 1732 1927 15383701 15383888 3.790000e-24 122.0
31 TraesCS5A01G461200 chr2B 79.167 168 31 3 1767 1930 59247027 59246860 2.280000e-21 113.0
32 TraesCS5A01G461200 chr7D 82.243 107 19 0 1727 1833 38466027 38466133 2.970000e-15 93.5
33 TraesCS5A01G461200 chr6B 78.676 136 25 4 1823 1955 715981534 715981400 1.380000e-13 87.9


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 TraesCS5A01G461200 chr5A 641675026 641677829 2803 False 5179.000000 5179 100.000000 1 2804 1 chr5A.!!$F1 2803
1 TraesCS5A01G461200 chr5A 359036565 359037300 735 True 1107.000000 1107 93.767000 1 738 1 chr5A.!!$R2 737
2 TraesCS5A01G461200 chr5A 563372247 563374922 2675 True 352.333333 436 93.891667 6 746 3 chr5A.!!$R3 740
3 TraesCS5A01G461200 chr7A 57088216 57088952 736 False 1079.000000 1079 93.080000 11 747 1 chr7A.!!$F1 736
4 TraesCS5A01G461200 chr5B 644852872 644857576 4704 False 654.500000 953 87.548250 849 2802 4 chr5B.!!$F1 1953
5 TraesCS5A01G461200 chr5D 513893800 513900030 6230 False 567.500000 885 90.634000 844 2804 4 chr5D.!!$F2 1960

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
771 2765 0.028642 AGGCTATGATTCCCACCCCT 60.029 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 7469 0.039437 GCCCGTCGTCATCATATCGT 60.039 55.0 0.0 0.0 0.0 3.73 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
65 66 2.576053 CGTCGCACGCGTATGTCT 60.576 61.111 13.44 0.00 40.74 3.41
78 79 3.554960 GCGTATGTCTCTAATCCATGGCA 60.555 47.826 6.96 0.00 0.00 4.92
310 2304 1.421268 TGCATCCTTCAGAACAGGTGT 59.579 47.619 0.00 0.00 32.59 4.16
380 2374 1.286553 ACTGAAGGAGAGACGAGGGAT 59.713 52.381 0.00 0.00 0.00 3.85
426 2420 0.037697 CGTGAGTTCATCGGTCCCAA 60.038 55.000 0.00 0.00 0.00 4.12
453 2447 8.563289 TTTTTACAAATAGTTTGCTGGTAACG 57.437 30.769 2.54 0.00 44.39 3.18
454 2448 7.493743 TTTACAAATAGTTTGCTGGTAACGA 57.506 32.000 2.54 0.00 44.39 3.85
486 2480 8.832735 TGTATATCCCTTTAGTCTTGTTTTCCT 58.167 33.333 0.00 0.00 0.00 3.36
543 2537 6.547141 AGAAGTCATGTGTTTCAAGATCCAAA 59.453 34.615 0.00 0.00 0.00 3.28
548 2542 9.643693 GTCATGTGTTTCAAGATCCAAATTATT 57.356 29.630 0.00 0.00 0.00 1.40
711 2705 6.429521 AAGTAGGCCTCAGTTTAGTGTTTA 57.570 37.500 9.68 0.00 0.00 2.01
758 2752 4.227134 CCCTGCGCACGAGGCTAT 62.227 66.667 5.66 0.00 41.67 2.97
759 2753 2.963854 CCTGCGCACGAGGCTATG 60.964 66.667 5.66 0.00 41.67 2.23
760 2754 2.104928 CTGCGCACGAGGCTATGA 59.895 61.111 5.66 0.00 41.67 2.15
761 2755 1.300465 CTGCGCACGAGGCTATGAT 60.300 57.895 5.66 0.00 41.67 2.45
762 2756 0.877649 CTGCGCACGAGGCTATGATT 60.878 55.000 5.66 0.00 41.67 2.57
763 2757 0.875908 TGCGCACGAGGCTATGATTC 60.876 55.000 5.66 0.00 41.67 2.52
764 2758 1.560860 GCGCACGAGGCTATGATTCC 61.561 60.000 0.30 0.00 41.67 3.01
765 2759 0.946221 CGCACGAGGCTATGATTCCC 60.946 60.000 2.51 0.00 41.67 3.97
766 2760 0.106708 GCACGAGGCTATGATTCCCA 59.893 55.000 2.51 0.00 40.25 4.37
767 2761 1.871080 CACGAGGCTATGATTCCCAC 58.129 55.000 0.00 0.00 0.00 4.61
768 2762 0.759346 ACGAGGCTATGATTCCCACC 59.241 55.000 0.00 0.00 0.00 4.61
769 2763 0.035458 CGAGGCTATGATTCCCACCC 59.965 60.000 0.00 0.00 0.00 4.61
770 2764 0.402121 GAGGCTATGATTCCCACCCC 59.598 60.000 0.00 0.00 0.00 4.95
771 2765 0.028642 AGGCTATGATTCCCACCCCT 60.029 55.000 0.00 0.00 0.00 4.79
772 2766 1.225694 AGGCTATGATTCCCACCCCTA 59.774 52.381 0.00 0.00 0.00 3.53
773 2767 2.157786 AGGCTATGATTCCCACCCCTAT 60.158 50.000 0.00 0.00 0.00 2.57
774 2768 3.080619 AGGCTATGATTCCCACCCCTATA 59.919 47.826 0.00 0.00 0.00 1.31
775 2769 3.200165 GGCTATGATTCCCACCCCTATAC 59.800 52.174 0.00 0.00 0.00 1.47
776 2770 3.200165 GCTATGATTCCCACCCCTATACC 59.800 52.174 0.00 0.00 0.00 2.73
777 2771 3.674358 ATGATTCCCACCCCTATACCT 57.326 47.619 0.00 0.00 0.00 3.08
778 2772 3.448277 TGATTCCCACCCCTATACCTT 57.552 47.619 0.00 0.00 0.00 3.50
779 2773 3.754976 TGATTCCCACCCCTATACCTTT 58.245 45.455 0.00 0.00 0.00 3.11
780 2774 4.123745 TGATTCCCACCCCTATACCTTTT 58.876 43.478 0.00 0.00 0.00 2.27
781 2775 4.546605 TGATTCCCACCCCTATACCTTTTT 59.453 41.667 0.00 0.00 0.00 1.94
805 2799 4.736126 TTTCTCTCCGTCTATCAATGCA 57.264 40.909 0.00 0.00 0.00 3.96
806 2800 4.736126 TTCTCTCCGTCTATCAATGCAA 57.264 40.909 0.00 0.00 0.00 4.08
807 2801 4.944619 TCTCTCCGTCTATCAATGCAAT 57.055 40.909 0.00 0.00 0.00 3.56
808 2802 4.625028 TCTCTCCGTCTATCAATGCAATG 58.375 43.478 0.00 0.00 0.00 2.82
809 2803 4.342092 TCTCTCCGTCTATCAATGCAATGA 59.658 41.667 6.97 6.97 0.00 2.57
810 2804 5.011431 TCTCTCCGTCTATCAATGCAATGAT 59.989 40.000 20.55 20.55 42.52 2.45
811 2805 6.209391 TCTCTCCGTCTATCAATGCAATGATA 59.791 38.462 20.58 20.58 40.44 2.15
812 2806 6.159293 TCTCCGTCTATCAATGCAATGATAC 58.841 40.000 18.52 12.63 40.44 2.24
813 2807 4.923281 TCCGTCTATCAATGCAATGATACG 59.077 41.667 23.86 23.86 39.63 3.06
814 2808 4.434725 CCGTCTATCAATGCAATGATACGC 60.435 45.833 24.80 16.97 39.06 4.42
815 2809 4.386954 CGTCTATCAATGCAATGATACGCT 59.613 41.667 20.97 4.06 40.44 5.07
816 2810 5.107337 CGTCTATCAATGCAATGATACGCTT 60.107 40.000 20.97 3.43 40.44 4.68
817 2811 6.302615 GTCTATCAATGCAATGATACGCTTC 58.697 40.000 18.52 5.99 40.44 3.86
818 2812 3.969117 TCAATGCAATGATACGCTTCC 57.031 42.857 0.00 0.00 0.00 3.46
819 2813 3.544684 TCAATGCAATGATACGCTTCCT 58.455 40.909 0.00 0.00 0.00 3.36
820 2814 3.947196 TCAATGCAATGATACGCTTCCTT 59.053 39.130 0.00 0.00 0.00 3.36
821 2815 5.122519 TCAATGCAATGATACGCTTCCTTA 58.877 37.500 0.00 0.00 0.00 2.69
822 2816 5.237127 TCAATGCAATGATACGCTTCCTTAG 59.763 40.000 0.00 0.00 0.00 2.18
823 2817 2.872245 TGCAATGATACGCTTCCTTAGC 59.128 45.455 0.00 0.00 46.83 3.09
833 2827 3.351020 GCTTCCTTAGCGTATTCGAGA 57.649 47.619 0.00 0.00 40.71 4.04
834 2828 3.703420 GCTTCCTTAGCGTATTCGAGAA 58.297 45.455 0.00 0.00 40.71 2.87
835 2829 4.110482 GCTTCCTTAGCGTATTCGAGAAA 58.890 43.478 0.00 0.00 40.71 2.52
836 2830 4.565564 GCTTCCTTAGCGTATTCGAGAAAA 59.434 41.667 0.00 0.00 40.71 2.29
837 2831 5.063060 GCTTCCTTAGCGTATTCGAGAAAAA 59.937 40.000 0.00 0.00 40.71 1.94
888 2882 2.159296 TCAGATGTACGAACGGTGGATG 60.159 50.000 0.00 0.00 0.00 3.51
904 2898 0.882042 GATGCGCCACCGATCATCTT 60.882 55.000 4.18 0.00 33.77 2.40
956 2955 0.548510 TTCACCACCATCACCACACA 59.451 50.000 0.00 0.00 0.00 3.72
957 2956 0.548510 TCACCACCATCACCACACAA 59.451 50.000 0.00 0.00 0.00 3.33
958 2957 0.667993 CACCACCATCACCACACAAC 59.332 55.000 0.00 0.00 0.00 3.32
959 2958 0.257328 ACCACCATCACCACACAACA 59.743 50.000 0.00 0.00 0.00 3.33
960 2959 0.667993 CCACCATCACCACACAACAC 59.332 55.000 0.00 0.00 0.00 3.32
961 2960 1.387539 CACCATCACCACACAACACA 58.612 50.000 0.00 0.00 0.00 3.72
962 2961 1.955778 CACCATCACCACACAACACAT 59.044 47.619 0.00 0.00 0.00 3.21
963 2962 3.145286 CACCATCACCACACAACACATA 58.855 45.455 0.00 0.00 0.00 2.29
964 2963 3.058293 CACCATCACCACACAACACATAC 60.058 47.826 0.00 0.00 0.00 2.39
965 2964 2.487762 CCATCACCACACAACACATACC 59.512 50.000 0.00 0.00 0.00 2.73
966 2965 1.872388 TCACCACACAACACATACCG 58.128 50.000 0.00 0.00 0.00 4.02
967 2966 1.413077 TCACCACACAACACATACCGA 59.587 47.619 0.00 0.00 0.00 4.69
968 2967 2.037902 TCACCACACAACACATACCGAT 59.962 45.455 0.00 0.00 0.00 4.18
969 2968 2.415168 CACCACACAACACATACCGATC 59.585 50.000 0.00 0.00 0.00 3.69
980 2979 4.635765 ACACATACCGATCATCCAAGTTTG 59.364 41.667 0.00 0.00 0.00 2.93
1066 4524 0.755698 GGTCCTCGTCATAGGGAGCA 60.756 60.000 0.00 0.00 44.24 4.26
1288 4746 0.598065 CCCCAGACTTTTTCTTGCGG 59.402 55.000 0.00 0.00 28.96 5.69
1290 4748 2.162681 CCCAGACTTTTTCTTGCGGAT 58.837 47.619 0.00 0.00 28.96 4.18
1314 4772 2.182030 GCCTCCGACCTTCTCACG 59.818 66.667 0.00 0.00 0.00 4.35
1332 4790 1.291877 CGAGCAACGGTAAGCAAGCT 61.292 55.000 8.00 0.00 38.46 3.74
1350 4808 0.824109 CTACCACCAATCGAGCTCCA 59.176 55.000 8.47 0.00 0.00 3.86
1363 4821 3.947196 TCGAGCTCCATGCATGTTAATTT 59.053 39.130 24.58 5.74 45.94 1.82
1365 4823 5.104374 CGAGCTCCATGCATGTTAATTTTT 58.896 37.500 24.58 2.63 45.94 1.94
1366 4824 5.230726 CGAGCTCCATGCATGTTAATTTTTC 59.769 40.000 24.58 10.11 45.94 2.29
1367 4825 6.290294 AGCTCCATGCATGTTAATTTTTCT 57.710 33.333 24.58 6.14 45.94 2.52
1368 4826 6.335777 AGCTCCATGCATGTTAATTTTTCTC 58.664 36.000 24.58 1.61 45.94 2.87
1369 4827 5.230726 GCTCCATGCATGTTAATTTTTCTCG 59.769 40.000 24.58 5.28 42.31 4.04
1370 4828 6.266168 TCCATGCATGTTAATTTTTCTCGT 57.734 33.333 24.58 0.00 0.00 4.18
1371 4829 6.686630 TCCATGCATGTTAATTTTTCTCGTT 58.313 32.000 24.58 0.00 0.00 3.85
1372 4830 7.821652 TCCATGCATGTTAATTTTTCTCGTTA 58.178 30.769 24.58 0.00 0.00 3.18
1373 4831 7.753132 TCCATGCATGTTAATTTTTCTCGTTAC 59.247 33.333 24.58 0.00 0.00 2.50
1374 4832 7.253288 CCATGCATGTTAATTTTTCTCGTTACG 60.253 37.037 24.58 0.00 0.00 3.18
1375 4833 6.660722 TGCATGTTAATTTTTCTCGTTACGT 58.339 32.000 4.24 0.00 0.00 3.57
1376 4834 7.794880 TGCATGTTAATTTTTCTCGTTACGTA 58.205 30.769 4.24 0.00 0.00 3.57
1377 4835 7.741216 TGCATGTTAATTTTTCTCGTTACGTAC 59.259 33.333 4.24 0.00 0.00 3.67
1413 4871 9.124807 GCCATGTTTTCAAGTTACAAGTAATAC 57.875 33.333 0.00 0.00 0.00 1.89
1452 4916 1.452145 TTTTGCCAGCCGTTGAGGTC 61.452 55.000 0.00 0.00 43.70 3.85
1489 4953 0.798771 GTGCTCGTCCATCGTCTGTC 60.799 60.000 0.00 0.00 40.80 3.51
1514 4978 2.120232 CATGCGCAACGGTAAACAAAA 58.880 42.857 17.11 0.00 0.00 2.44
1515 4979 1.546834 TGCGCAACGGTAAACAAAAC 58.453 45.000 8.16 0.00 0.00 2.43
1524 4988 7.940435 CGCAACGGTAAACAAAACAAATATTAC 59.060 33.333 0.00 0.00 0.00 1.89
1528 4992 8.298854 ACGGTAAACAAAACAAATATTACCTCC 58.701 33.333 9.92 0.00 39.90 4.30
1533 4997 5.416639 ACAAAACAAATATTACCTCCGTCCC 59.583 40.000 0.00 0.00 0.00 4.46
1534 4998 3.464111 ACAAATATTACCTCCGTCCCG 57.536 47.619 0.00 0.00 0.00 5.14
1540 5004 5.656213 ATATTACCTCCGTCCCGAATTAG 57.344 43.478 0.00 0.00 0.00 1.73
1545 5009 2.268298 CTCCGTCCCGAATTAGTTGTG 58.732 52.381 0.00 0.00 0.00 3.33
1549 5013 4.081531 TCCGTCCCGAATTAGTTGTGTTAT 60.082 41.667 0.00 0.00 0.00 1.89
1556 5020 8.885722 TCCCGAATTAGTTGTGTTATATTTGTC 58.114 33.333 0.00 0.00 0.00 3.18
1557 5021 8.889717 CCCGAATTAGTTGTGTTATATTTGTCT 58.110 33.333 0.00 0.00 0.00 3.41
1575 5039 5.948992 TGTCTAGATACATCGTGATGGAG 57.051 43.478 13.95 3.96 42.91 3.86
1586 5050 6.480763 ACATCGTGATGGAGAGAGTAGATAT 58.519 40.000 13.95 0.00 42.91 1.63
1587 5051 7.625469 ACATCGTGATGGAGAGAGTAGATATA 58.375 38.462 13.95 0.00 42.91 0.86
1634 5099 3.273009 CGTCTAACGCGCGTACTG 58.727 61.111 37.93 26.76 33.65 2.74
1635 5100 1.510623 CGTCTAACGCGCGTACTGT 60.511 57.895 37.93 23.31 33.65 3.55
1636 5101 0.247262 CGTCTAACGCGCGTACTGTA 60.247 55.000 37.93 23.16 33.65 2.74
1637 5102 1.593070 CGTCTAACGCGCGTACTGTAT 60.593 52.381 37.93 22.07 33.65 2.29
1638 5103 2.032652 GTCTAACGCGCGTACTGTATC 58.967 52.381 37.93 18.15 0.00 2.24
1639 5104 1.935873 TCTAACGCGCGTACTGTATCT 59.064 47.619 37.93 20.44 0.00 1.98
1640 5105 2.034789 CTAACGCGCGTACTGTATCTG 58.965 52.381 37.93 11.82 0.00 2.90
1641 5106 0.169672 AACGCGCGTACTGTATCTGT 59.830 50.000 37.93 13.90 0.00 3.41
1642 5107 1.009078 ACGCGCGTACTGTATCTGTA 58.991 50.000 37.08 0.00 0.00 2.74
1643 5108 1.600957 ACGCGCGTACTGTATCTGTAT 59.399 47.619 37.08 3.21 0.00 2.29
1669 5134 2.503331 TGTATGTTCTGGCACCAGTTG 58.497 47.619 16.12 0.00 43.96 3.16
1757 7419 1.667830 CAACTGCGTCGTGGTGGAT 60.668 57.895 0.00 0.00 0.00 3.41
1758 7420 1.667830 AACTGCGTCGTGGTGGATG 60.668 57.895 0.00 0.00 0.00 3.51
1793 7455 1.068264 CACGACGGATCCATCATCGAT 60.068 52.381 23.75 0.00 38.47 3.59
1798 7460 3.095332 ACGGATCCATCATCGATCTCAT 58.905 45.455 13.41 0.00 37.02 2.90
1807 7469 4.385358 TCATCGATCTCATTTTGACCGA 57.615 40.909 0.00 0.00 0.00 4.69
1812 7474 4.035909 TCGATCTCATTTTGACCGACGATA 59.964 41.667 0.00 0.00 0.00 2.92
1818 7480 5.596845 TCATTTTGACCGACGATATGATGA 58.403 37.500 0.00 0.00 29.66 2.92
1829 7491 1.542030 GATATGATGACGACGGGCTCT 59.458 52.381 0.00 0.00 0.00 4.09
1833 7495 1.934220 GATGACGACGGGCTCTGACA 61.934 60.000 0.00 0.00 0.00 3.58
1852 7514 4.018506 TGACAAGAAAGAATAGGGCATGGA 60.019 41.667 0.00 0.00 0.00 3.41
1873 7535 2.527951 GATGGTGGCGCCTTGAGTCT 62.528 60.000 29.70 5.51 38.35 3.24
1915 7577 1.822613 CTACTCTACCTCGCCGGCA 60.823 63.158 28.98 12.94 35.61 5.69
1943 7606 2.928396 ACTTGGGCGGGTGTAGCT 60.928 61.111 0.00 0.00 34.52 3.32
1967 7630 1.203052 CGCTGGACGGTCTTTACCTAA 59.797 52.381 8.23 0.00 44.35 2.69
1999 7662 7.063308 GGTTTCACTTTGCATGTAATTGTATGG 59.937 37.037 0.00 0.00 0.00 2.74
2009 7672 7.341512 TGCATGTAATTGTATGGATTTGAGGAA 59.658 33.333 0.00 0.00 0.00 3.36
2020 7683 6.677781 TGGATTTGAGGAATCGTAATTGTC 57.322 37.500 0.00 0.00 44.21 3.18
2021 7684 6.176896 TGGATTTGAGGAATCGTAATTGTCA 58.823 36.000 0.00 0.00 44.21 3.58
2043 7706 8.729756 TGTCATATCTGGTTGTGAAAATGTTAG 58.270 33.333 0.00 0.00 0.00 2.34
2049 7712 6.153680 TCTGGTTGTGAAAATGTTAGTTTGGT 59.846 34.615 0.00 0.00 0.00 3.67
2100 7763 1.069513 CGGATTTGATGTACCCGGCTA 59.930 52.381 0.00 0.00 36.81 3.93
2112 7775 3.468071 ACCCGGCTAGATGTATGGATA 57.532 47.619 0.00 0.00 0.00 2.59
2137 7800 5.457686 AGATGCTCTAAGATTCTGAGACCT 58.542 41.667 0.00 0.00 0.00 3.85
2217 7880 9.076596 GTACCACGTACGTAAATTAAAGAGAAT 57.923 33.333 22.34 0.00 29.20 2.40
2237 7900 9.030452 AGAGAATTATAGATATTGAGCGACCTT 57.970 33.333 0.00 0.00 0.00 3.50
2259 7922 2.509052 TCTTAATCTCCATCGCACCG 57.491 50.000 0.00 0.00 0.00 4.94
2283 7946 4.500545 GCATCACAATCGACTATCCTCACT 60.501 45.833 0.00 0.00 0.00 3.41
2337 8000 9.998106 ATATTTGACACTTTCCGTAGCTATATT 57.002 29.630 0.00 0.00 0.00 1.28
2357 8020 1.202651 TCCTCTATTGCTAAAGGGCGC 60.203 52.381 0.00 0.00 34.52 6.53
2445 10471 3.181483 CCATGGCTTGATGGTTTTAGCTC 60.181 47.826 0.00 0.00 38.53 4.09
2462 10488 8.488764 GTTTTAGCTCGTTATATAAAGCTCAGG 58.511 37.037 20.08 4.01 43.72 3.86
2475 10501 2.525368 AGCTCAGGCCGGTTAAAATTT 58.475 42.857 1.90 0.00 39.73 1.82
2484 10510 3.729762 GCCGGTTAAAATTTCGCCTAGTG 60.730 47.826 1.90 0.00 0.00 2.74
2486 10512 4.201783 CCGGTTAAAATTTCGCCTAGTGAG 60.202 45.833 0.00 0.00 0.00 3.51
2496 10522 2.095364 TCGCCTAGTGAGAACGAAGAAC 60.095 50.000 0.00 0.00 30.96 3.01
2592 10618 0.106967 GAAGCCATCTCAACCCTCCC 60.107 60.000 0.00 0.00 0.00 4.30
2607 10633 2.500098 CCCTCCCTGAAACGAGTAATCA 59.500 50.000 0.00 0.00 0.00 2.57
2633 10659 2.842939 GCAAAGATTTTGCGCAAGTC 57.157 45.000 23.68 23.02 41.68 3.01
2646 10672 0.526211 GCAAGTCGATTTTGGGGGAC 59.474 55.000 12.65 0.00 0.00 4.46
2652 10678 3.585732 AGTCGATTTTGGGGGACTTAGAA 59.414 43.478 0.00 0.00 36.39 2.10
2653 10679 4.042435 AGTCGATTTTGGGGGACTTAGAAA 59.958 41.667 0.00 0.00 36.39 2.52
2654 10680 4.948004 GTCGATTTTGGGGGACTTAGAAAT 59.052 41.667 0.00 0.00 0.00 2.17
2655 10681 6.069847 AGTCGATTTTGGGGGACTTAGAAATA 60.070 38.462 0.00 0.00 36.39 1.40
2656 10682 6.771267 GTCGATTTTGGGGGACTTAGAAATAT 59.229 38.462 0.00 0.00 0.00 1.28
2657 10683 6.996282 TCGATTTTGGGGGACTTAGAAATATC 59.004 38.462 0.00 0.00 0.00 1.63
2658 10684 6.770785 CGATTTTGGGGGACTTAGAAATATCA 59.229 38.462 0.00 0.00 0.00 2.15
2659 10685 7.448469 CGATTTTGGGGGACTTAGAAATATCAT 59.552 37.037 0.00 0.00 0.00 2.45
2720 10746 1.518572 GTGCGAGGTGGGTATCACG 60.519 63.158 0.00 0.00 46.96 4.35
2725 10751 1.997606 CGAGGTGGGTATCACGTTTTC 59.002 52.381 0.00 0.00 46.96 2.29
2728 10754 4.070009 GAGGTGGGTATCACGTTTTCTTT 58.930 43.478 0.00 0.00 46.96 2.52
2729 10755 4.466827 AGGTGGGTATCACGTTTTCTTTT 58.533 39.130 0.00 0.00 46.96 2.27
2730 10756 4.517832 AGGTGGGTATCACGTTTTCTTTTC 59.482 41.667 0.00 0.00 46.96 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 7.365921 GGGTATTCTCATATGCCATGGATTAGA 60.366 40.741 18.40 3.75 32.48 2.10
78 79 4.021456 TGCGAACGATGGGTATTCTCATAT 60.021 41.667 0.00 0.00 0.00 1.78
121 122 1.742880 TTGCATCTGTCGAGCAGCC 60.743 57.895 9.34 3.21 44.66 4.85
126 127 1.354040 GTCAGGTTGCATCTGTCGAG 58.646 55.000 14.61 0.00 34.15 4.04
310 2304 5.410439 GGGAAAGTAACAACAAGCGAGATAA 59.590 40.000 0.00 0.00 0.00 1.75
626 2620 7.062371 CCGATAAGTCCTTTATGATGTCGAATC 59.938 40.741 0.00 0.00 32.09 2.52
631 2625 8.142551 AGTTACCGATAAGTCCTTTATGATGTC 58.857 37.037 0.00 0.00 32.09 3.06
711 2705 0.112412 AAAATTCGGGACCCTGTGCT 59.888 50.000 9.41 0.00 0.00 4.40
720 2714 3.065567 GGCCGGCAAAATTCGGGA 61.066 61.111 30.85 0.00 45.75 5.14
747 2741 0.106708 TGGGAATCATAGCCTCGTGC 59.893 55.000 0.00 0.00 41.71 5.34
748 2742 1.541233 GGTGGGAATCATAGCCTCGTG 60.541 57.143 0.00 0.00 0.00 4.35
749 2743 0.759346 GGTGGGAATCATAGCCTCGT 59.241 55.000 0.00 0.00 0.00 4.18
750 2744 0.035458 GGGTGGGAATCATAGCCTCG 59.965 60.000 0.00 0.00 0.00 4.63
751 2745 0.402121 GGGGTGGGAATCATAGCCTC 59.598 60.000 4.65 0.00 32.73 4.70
752 2746 0.028642 AGGGGTGGGAATCATAGCCT 60.029 55.000 4.65 0.00 32.73 4.58
753 2747 1.742308 TAGGGGTGGGAATCATAGCC 58.258 55.000 0.00 0.00 0.00 3.93
754 2748 3.200165 GGTATAGGGGTGGGAATCATAGC 59.800 52.174 0.00 0.00 0.00 2.97
755 2749 4.699994 AGGTATAGGGGTGGGAATCATAG 58.300 47.826 0.00 0.00 0.00 2.23
756 2750 4.796185 AGGTATAGGGGTGGGAATCATA 57.204 45.455 0.00 0.00 0.00 2.15
757 2751 3.674358 AGGTATAGGGGTGGGAATCAT 57.326 47.619 0.00 0.00 0.00 2.45
758 2752 3.448277 AAGGTATAGGGGTGGGAATCA 57.552 47.619 0.00 0.00 0.00 2.57
759 2753 4.808767 AAAAGGTATAGGGGTGGGAATC 57.191 45.455 0.00 0.00 0.00 2.52
782 2776 5.487433 TGCATTGATAGACGGAGAGAAAAA 58.513 37.500 0.00 0.00 0.00 1.94
783 2777 5.084818 TGCATTGATAGACGGAGAGAAAA 57.915 39.130 0.00 0.00 0.00 2.29
784 2778 4.736126 TGCATTGATAGACGGAGAGAAA 57.264 40.909 0.00 0.00 0.00 2.52
785 2779 4.736126 TTGCATTGATAGACGGAGAGAA 57.264 40.909 0.00 0.00 0.00 2.87
786 2780 4.342092 TCATTGCATTGATAGACGGAGAGA 59.658 41.667 7.19 0.00 0.00 3.10
787 2781 4.625028 TCATTGCATTGATAGACGGAGAG 58.375 43.478 7.19 0.00 0.00 3.20
788 2782 4.670896 TCATTGCATTGATAGACGGAGA 57.329 40.909 7.19 0.00 0.00 3.71
789 2783 5.061435 CGTATCATTGCATTGATAGACGGAG 59.939 44.000 25.28 13.93 38.83 4.63
790 2784 4.923281 CGTATCATTGCATTGATAGACGGA 59.077 41.667 25.28 10.46 38.83 4.69
791 2785 4.434725 GCGTATCATTGCATTGATAGACGG 60.435 45.833 29.49 20.45 38.83 4.79
792 2786 4.386954 AGCGTATCATTGCATTGATAGACG 59.613 41.667 27.03 27.03 38.83 4.18
793 2787 5.852738 AGCGTATCATTGCATTGATAGAC 57.147 39.130 24.60 19.93 38.83 2.59
794 2788 5.409520 GGAAGCGTATCATTGCATTGATAGA 59.590 40.000 24.60 9.88 38.83 1.98
795 2789 5.410746 AGGAAGCGTATCATTGCATTGATAG 59.589 40.000 24.60 19.64 38.83 2.08
796 2790 5.308014 AGGAAGCGTATCATTGCATTGATA 58.692 37.500 21.66 21.66 37.51 2.15
797 2791 4.139786 AGGAAGCGTATCATTGCATTGAT 58.860 39.130 23.42 23.42 39.60 2.57
798 2792 3.544684 AGGAAGCGTATCATTGCATTGA 58.455 40.909 13.30 13.30 0.00 2.57
799 2793 3.976793 AGGAAGCGTATCATTGCATTG 57.023 42.857 2.08 2.08 0.00 2.82
800 2794 4.023707 GCTAAGGAAGCGTATCATTGCATT 60.024 41.667 0.00 0.00 42.53 3.56
801 2795 3.499918 GCTAAGGAAGCGTATCATTGCAT 59.500 43.478 0.00 0.00 42.53 3.96
802 2796 2.872245 GCTAAGGAAGCGTATCATTGCA 59.128 45.455 0.00 0.00 42.53 4.08
803 2797 3.528009 GCTAAGGAAGCGTATCATTGC 57.472 47.619 0.77 0.08 42.53 3.56
814 2808 6.642683 TTTTTCTCGAATACGCTAAGGAAG 57.357 37.500 0.00 0.00 39.58 3.46
838 2832 4.826733 TGATGAGTGTGCATGGTACTTTTT 59.173 37.500 0.00 0.00 0.00 1.94
839 2833 4.397420 TGATGAGTGTGCATGGTACTTTT 58.603 39.130 0.00 0.00 0.00 2.27
840 2834 4.019792 TGATGAGTGTGCATGGTACTTT 57.980 40.909 0.00 0.00 0.00 2.66
841 2835 3.701205 TGATGAGTGTGCATGGTACTT 57.299 42.857 0.00 0.00 0.00 2.24
842 2836 3.701205 TTGATGAGTGTGCATGGTACT 57.299 42.857 0.00 0.00 0.00 2.73
888 2882 0.032130 TAGAAGATGATCGGTGGCGC 59.968 55.000 0.00 0.00 0.00 6.53
894 2888 7.067129 TCGGTCCTATTTATAGAAGATGATCGG 59.933 40.741 0.00 0.00 32.05 4.18
904 2898 5.182570 CGTGTGGATCGGTCCTATTTATAGA 59.817 44.000 17.40 0.00 45.32 1.98
926 2920 2.925724 TGGTGGTGAAACAAGAATCGT 58.074 42.857 0.00 0.00 39.98 3.73
956 2955 4.487714 ACTTGGATGATCGGTATGTGTT 57.512 40.909 0.00 0.00 0.00 3.32
957 2956 4.487714 AACTTGGATGATCGGTATGTGT 57.512 40.909 0.00 0.00 0.00 3.72
958 2957 4.875536 TCAAACTTGGATGATCGGTATGTG 59.124 41.667 0.00 0.00 0.00 3.21
959 2958 5.097742 TCAAACTTGGATGATCGGTATGT 57.902 39.130 0.00 0.00 0.00 2.29
960 2959 4.024556 GCTCAAACTTGGATGATCGGTATG 60.025 45.833 0.00 0.00 0.00 2.39
961 2960 4.130118 GCTCAAACTTGGATGATCGGTAT 58.870 43.478 0.00 0.00 0.00 2.73
962 2961 3.197766 AGCTCAAACTTGGATGATCGGTA 59.802 43.478 0.00 0.00 0.00 4.02
963 2962 2.026822 AGCTCAAACTTGGATGATCGGT 60.027 45.455 0.00 0.00 0.00 4.69
964 2963 2.353889 CAGCTCAAACTTGGATGATCGG 59.646 50.000 0.00 0.00 0.00 4.18
965 2964 2.223203 GCAGCTCAAACTTGGATGATCG 60.223 50.000 0.00 0.00 0.00 3.69
966 2965 2.751259 TGCAGCTCAAACTTGGATGATC 59.249 45.455 0.00 0.00 0.00 2.92
967 2966 2.490903 GTGCAGCTCAAACTTGGATGAT 59.509 45.455 0.00 0.00 0.00 2.45
968 2967 1.881973 GTGCAGCTCAAACTTGGATGA 59.118 47.619 0.00 0.00 0.00 2.92
969 2968 1.400629 CGTGCAGCTCAAACTTGGATG 60.401 52.381 0.00 0.00 0.00 3.51
980 2979 3.659291 CGTACGTACGTGCAGCTC 58.341 61.111 33.95 13.85 44.13 4.09
1297 4755 2.182030 CGTGAGAAGGTCGGAGGC 59.818 66.667 0.00 0.00 0.00 4.70
1314 4772 1.393883 GTAGCTTGCTTACCGTTGCTC 59.606 52.381 0.00 0.00 32.72 4.26
1332 4790 1.138859 CATGGAGCTCGATTGGTGGTA 59.861 52.381 8.71 0.00 0.00 3.25
1350 4808 7.302524 ACGTAACGAGAAAAATTAACATGCAT 58.697 30.769 0.00 0.00 0.00 3.96
1387 4845 9.124807 GTATTACTTGTAACTTGAAAACATGGC 57.875 33.333 0.00 0.00 0.00 4.40
1413 4871 5.598416 AAAAGGGAAAACAAGAGAGTTGG 57.402 39.130 0.00 0.00 0.00 3.77
1489 4953 2.181372 TTACCGTTGCGCATGCTGTG 62.181 55.000 12.75 0.81 43.34 3.66
1549 5013 8.404107 TCCATCACGATGTATCTAGACAAATA 57.596 34.615 0.00 0.00 37.11 1.40
1556 5020 5.937540 ACTCTCTCCATCACGATGTATCTAG 59.062 44.000 6.30 1.60 37.11 2.43
1557 5021 5.870706 ACTCTCTCCATCACGATGTATCTA 58.129 41.667 6.30 0.00 37.11 1.98
1634 5099 9.847706 CCAGAACATACATACAGATACAGATAC 57.152 37.037 0.00 0.00 0.00 2.24
1635 5100 8.523658 GCCAGAACATACATACAGATACAGATA 58.476 37.037 0.00 0.00 0.00 1.98
1636 5101 7.015584 TGCCAGAACATACATACAGATACAGAT 59.984 37.037 0.00 0.00 0.00 2.90
1637 5102 6.323739 TGCCAGAACATACATACAGATACAGA 59.676 38.462 0.00 0.00 0.00 3.41
1638 5103 6.422100 GTGCCAGAACATACATACAGATACAG 59.578 42.308 0.00 0.00 0.00 2.74
1639 5104 6.280643 GTGCCAGAACATACATACAGATACA 58.719 40.000 0.00 0.00 0.00 2.29
1640 5105 5.696724 GGTGCCAGAACATACATACAGATAC 59.303 44.000 0.00 0.00 0.00 2.24
1641 5106 5.365314 TGGTGCCAGAACATACATACAGATA 59.635 40.000 0.00 0.00 0.00 1.98
1642 5107 4.164030 TGGTGCCAGAACATACATACAGAT 59.836 41.667 0.00 0.00 0.00 2.90
1643 5108 3.517500 TGGTGCCAGAACATACATACAGA 59.482 43.478 0.00 0.00 0.00 3.41
1743 7405 2.356913 CACATCCACCACGACGCA 60.357 61.111 0.00 0.00 0.00 5.24
1749 7411 2.746277 GGCCGACACATCCACCAC 60.746 66.667 0.00 0.00 0.00 4.16
1775 7437 1.470494 AGATCGATGATGGATCCGTCG 59.530 52.381 25.53 21.11 40.93 5.12
1793 7455 5.257082 TCATATCGTCGGTCAAAATGAGA 57.743 39.130 0.00 0.00 0.00 3.27
1798 7460 3.794564 CGTCATCATATCGTCGGTCAAAA 59.205 43.478 0.00 0.00 0.00 2.44
1807 7469 0.039437 GCCCGTCGTCATCATATCGT 60.039 55.000 0.00 0.00 0.00 3.73
1812 7474 1.037579 TCAGAGCCCGTCGTCATCAT 61.038 55.000 0.00 0.00 0.00 2.45
1818 7480 1.461091 TTCTTGTCAGAGCCCGTCGT 61.461 55.000 0.00 0.00 0.00 4.34
1829 7491 4.018506 TCCATGCCCTATTCTTTCTTGTCA 60.019 41.667 0.00 0.00 0.00 3.58
1833 7495 5.456921 TCTTCCATGCCCTATTCTTTCTT 57.543 39.130 0.00 0.00 0.00 2.52
1852 7514 1.377725 CTCAAGGCGCCACCATCTT 60.378 57.895 31.54 10.30 43.14 2.40
1873 7535 1.069090 GAGACACACCGGCTCACAA 59.931 57.895 0.00 0.00 0.00 3.33
1967 7630 9.777297 AATTACATGCAAAGTGAAACCTAATTT 57.223 25.926 5.51 0.00 37.80 1.82
1981 7644 7.980662 CCTCAAATCCATACAATTACATGCAAA 59.019 33.333 0.00 0.00 0.00 3.68
1982 7645 7.341512 TCCTCAAATCCATACAATTACATGCAA 59.658 33.333 0.00 0.00 0.00 4.08
1984 7647 7.275888 TCCTCAAATCCATACAATTACATGC 57.724 36.000 0.00 0.00 0.00 4.06
2009 7672 7.272244 TCACAACCAGATATGACAATTACGAT 58.728 34.615 0.00 0.00 0.00 3.73
2020 7683 9.912634 AAACTAACATTTTCACAACCAGATATG 57.087 29.630 0.00 0.00 0.00 1.78
2021 7684 9.912634 CAAACTAACATTTTCACAACCAGATAT 57.087 29.630 0.00 0.00 0.00 1.63
2025 7688 6.255453 CACCAAACTAACATTTTCACAACCAG 59.745 38.462 0.00 0.00 0.00 4.00
2049 7712 1.066929 CATCATGTCCACGGTCAGACA 60.067 52.381 11.66 11.66 46.39 3.41
2059 7722 3.621214 CGACCCCTTAAACATCATGTCCA 60.621 47.826 0.00 0.00 0.00 4.02
2217 7880 8.354711 AGATGAAGGTCGCTCAATATCTATAA 57.645 34.615 0.00 0.00 0.00 0.98
2237 7900 3.552890 CGGTGCGATGGAGATTAAGATGA 60.553 47.826 0.00 0.00 0.00 2.92
2259 7922 3.243873 TGAGGATAGTCGATTGTGATGCC 60.244 47.826 0.00 0.00 0.00 4.40
2283 7946 5.068198 GGTAGATGGTCACCGAACAATACTA 59.932 44.000 0.00 1.16 31.09 1.82
2320 7983 8.524487 CAATAGAGGAATATAGCTACGGAAAGT 58.476 37.037 0.00 0.00 0.00 2.66
2326 7989 9.509855 CTTTAGCAATAGAGGAATATAGCTACG 57.490 37.037 0.00 0.00 33.57 3.51
2337 8000 1.202651 GCGCCCTTTAGCAATAGAGGA 60.203 52.381 0.00 0.00 0.00 3.71
2445 10471 2.993899 CCGGCCTGAGCTTTATATAACG 59.006 50.000 0.00 0.00 39.73 3.18
2462 10488 2.421073 ACTAGGCGAAATTTTAACCGGC 59.579 45.455 13.50 13.50 45.93 6.13
2475 10501 1.817357 TCTTCGTTCTCACTAGGCGA 58.183 50.000 0.00 0.00 0.00 5.54
2484 10510 8.928270 TTTTAGATGGATAGTTCTTCGTTCTC 57.072 34.615 0.00 0.00 0.00 2.87
2581 10607 0.685097 TCGTTTCAGGGAGGGTTGAG 59.315 55.000 0.00 0.00 0.00 3.02
2582 10608 0.685097 CTCGTTTCAGGGAGGGTTGA 59.315 55.000 0.00 0.00 0.00 3.18
2592 10618 2.972625 TGGCCTGATTACTCGTTTCAG 58.027 47.619 3.32 0.00 37.27 3.02
2607 10633 1.673626 CGCAAAATCTTTGCATGGCCT 60.674 47.619 20.56 0.00 45.14 5.19
2609 10635 0.095762 GCGCAAAATCTTTGCATGGC 59.904 50.000 20.56 13.46 45.14 4.40
2611 10637 2.477375 ACTTGCGCAAAATCTTTGCATG 59.523 40.909 25.01 10.05 45.14 4.06
2633 10659 6.770785 TGATATTTCTAAGTCCCCCAAAATCG 59.229 38.462 0.00 0.00 0.00 3.34
2707 10733 3.782656 AAGAAAACGTGATACCCACCT 57.217 42.857 0.00 0.00 42.76 4.00
2728 10754 4.261155 CGTTTCTGGATGTTTTCTGCAGAA 60.261 41.667 25.16 25.16 33.46 3.02
2729 10755 3.250762 CGTTTCTGGATGTTTTCTGCAGA 59.749 43.478 13.74 13.74 0.00 4.26
2730 10756 3.558505 CGTTTCTGGATGTTTTCTGCAG 58.441 45.455 7.63 7.63 0.00 4.41
2769 10796 0.810648 TTCGCCAACATTCTGGATGC 59.189 50.000 0.00 0.00 38.96 3.91


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

AutoCloner maintained by Alex Coulton.