Multiple sequence alignment - TraesCS4B01G084600

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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 TraesCS4B01G084600 chr4B 100.000 3410 0 0 1 3410 82936297 82932888 0.000000e+00 6298.0
1 TraesCS4B01G084600 chr4B 89.610 77 5 3 951 1026 178372143 178372069 1.010000e-15 95.3
2 TraesCS4B01G084600 chr4D 94.920 1496 57 4 1031 2510 55965140 55963648 0.000000e+00 2324.0
3 TraesCS4B01G084600 chr4D 90.302 794 47 21 1 777 55967588 55966808 0.000000e+00 1013.0
4 TraesCS4B01G084600 chr4D 82.307 763 116 14 2553 3302 55716844 55716088 0.000000e+00 643.0
5 TraesCS4B01G084600 chr4D 87.393 468 57 1 2927 3392 56411324 56411791 1.390000e-148 536.0
6 TraesCS4B01G084600 chr4A 95.474 1392 63 0 1030 2421 540957702 540959093 0.000000e+00 2222.0
7 TraesCS4B01G084600 chr4A 86.138 945 102 15 2459 3388 540959922 540960852 0.000000e+00 992.0
8 TraesCS4B01G084600 chr4A 89.865 592 31 16 202 782 540952408 540952981 0.000000e+00 734.0
9 TraesCS4B01G084600 chr4A 84.579 642 65 11 2052 2677 540902334 540902957 1.050000e-169 606.0
10 TraesCS4B01G084600 chr4A 91.710 386 31 1 1322 1707 540846763 540847147 5.010000e-148 534.0
11 TraesCS4B01G084600 chr4A 88.316 291 34 0 1030 1320 540710400 540710690 1.950000e-92 350.0
12 TraesCS4B01G084600 chr6A 79.284 391 56 17 37 416 600947486 600947862 2.030000e-62 250.0
13 TraesCS4B01G084600 chr6D 94.074 135 8 0 1854 1988 33243274 33243408 4.460000e-49 206.0
14 TraesCS4B01G084600 chr6B 88.079 151 17 1 1855 2005 69955874 69956023 9.720000e-41 178.0
15 TraesCS4B01G084600 chr3B 91.139 79 6 1 955 1033 817135940 817135863 4.650000e-19 106.0
16 TraesCS4B01G084600 chr7A 90.789 76 6 1 955 1030 675100010 675100084 2.170000e-17 100.0
17 TraesCS4B01G084600 chr2A 95.238 63 3 0 3330 3392 41160095 41160157 2.170000e-17 100.0
18 TraesCS4B01G084600 chrUn 90.667 75 5 2 952 1026 85058638 85058566 7.790000e-17 99.0
19 TraesCS4B01G084600 chr5A 89.744 78 6 2 951 1026 6261260 6261183 7.790000e-17 99.0
20 TraesCS4B01G084600 chr5D 89.610 77 7 1 3317 3392 34240307 34240383 2.800000e-16 97.1
21 TraesCS4B01G084600 chr2B 92.424 66 5 0 3328 3393 542146157 542146222 1.010000e-15 95.3
22 TraesCS4B01G084600 chr2B 85.897 78 9 2 957 1033 51169115 51169039 7.840000e-12 82.4
23 TraesCS4B01G084600 chr7B 92.308 65 5 0 966 1030 125423008 125422944 3.620000e-15 93.5
24 TraesCS4B01G084600 chr1D 87.500 80 7 3 955 1033 206059839 206059762 4.690000e-14 89.8
25 TraesCS4B01G084600 chr1D 89.706 68 5 2 967 1033 207045103 207045037 6.060000e-13 86.1
26 TraesCS4B01G084600 chr1B 91.803 61 5 0 3333 3393 197695551 197695611 6.060000e-13 86.1
27 TraesCS4B01G084600 chr3D 82.540 63 11 0 3330 3392 522095493 522095431 4.750000e-04 56.5
28 TraesCS4B01G084600 chr3A 92.308 39 1 1 3339 3377 267072479 267072515 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 TraesCS4B01G084600 chr4B 82932888 82936297 3409 True 6298.0 6298 100.000 1 3410 1 chr4B.!!$R1 3409
1 TraesCS4B01G084600 chr4D 55963648 55967588 3940 True 1668.5 2324 92.611 1 2510 2 chr4D.!!$R2 2509
2 TraesCS4B01G084600 chr4D 55716088 55716844 756 True 643.0 643 82.307 2553 3302 1 chr4D.!!$R1 749
3 TraesCS4B01G084600 chr4A 540957702 540960852 3150 False 1607.0 2222 90.806 1030 3388 2 chr4A.!!$F5 2358
4 TraesCS4B01G084600 chr4A 540952408 540952981 573 False 734.0 734 89.865 202 782 1 chr4A.!!$F4 580
5 TraesCS4B01G084600 chr4A 540902334 540902957 623 False 606.0 606 84.579 2052 2677 1 chr4A.!!$F3 625

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
246 250 0.679960 GAGTGGCAACCATACCCCAC 60.680 60.0 0.0 0.57 46.22 4.61 F
849 2358 0.824759 ACTGCCGTATCTCCAACTCC 59.175 55.0 0.0 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 3255 1.433471 CTGCATGACGAGCGAGGTA 59.567 57.895 0.00 0.0 33.85 3.08 R
2427 4538 0.478072 TCCATGGGAAGCACTGTTGT 59.522 50.000 13.02 0.0 0.00 3.32 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
27 28 5.060662 TCAGAGTAGCACACATGTCTAAC 57.939 43.478 0.00 0.00 0.00 2.34
34 35 2.738846 GCACACATGTCTAACACTCCTG 59.261 50.000 0.00 0.00 0.00 3.86
60 61 8.135529 GGTTATGGTGATAAAAATAAGAGGCAC 58.864 37.037 0.00 0.00 0.00 5.01
67 68 7.270579 GTGATAAAAATAAGAGGCACGTGAAAC 59.729 37.037 22.23 8.55 0.00 2.78
103 104 5.912149 TCCCTAGATAAGGCAAATGTGAT 57.088 39.130 0.00 0.00 45.03 3.06
117 118 6.458206 GGCAAATGTGATCGCACTAAGATAAA 60.458 38.462 11.96 0.00 45.36 1.40
121 122 6.510746 TGTGATCGCACTAAGATAAATTCG 57.489 37.500 4.45 0.00 45.36 3.34
125 126 5.961395 TCGCACTAAGATAAATTCGGTTC 57.039 39.130 0.00 0.00 0.00 3.62
126 127 5.412640 TCGCACTAAGATAAATTCGGTTCA 58.587 37.500 0.00 0.00 0.00 3.18
158 159 3.214328 GACTTGACCAAGCCAAAGAAGA 58.786 45.455 9.48 0.00 41.99 2.87
162 163 2.091885 TGACCAAGCCAAAGAAGAGGTT 60.092 45.455 0.00 0.00 0.00 3.50
172 176 5.278022 GCCAAAGAAGAGGTTGACTAAACAG 60.278 44.000 0.00 0.00 40.86 3.16
245 249 1.136961 TGAGTGGCAACCATACCCCA 61.137 55.000 0.00 0.00 35.28 4.96
246 250 0.679960 GAGTGGCAACCATACCCCAC 60.680 60.000 0.00 0.57 46.22 4.61
249 253 2.043349 GCAACCATACCCCACCCC 60.043 66.667 0.00 0.00 0.00 4.95
250 254 2.687266 CAACCATACCCCACCCCC 59.313 66.667 0.00 0.00 0.00 5.40
295 299 5.426833 AGCATGGTCTACAAGGAGATAAAGT 59.573 40.000 0.00 0.00 0.00 2.66
497 502 6.091169 CCAAATCAAAATTCAACCAAGATCCG 59.909 38.462 0.00 0.00 0.00 4.18
640 647 5.856156 TGTGTTCTTTCTATTCCCACGTTA 58.144 37.500 0.00 0.00 0.00 3.18
644 651 7.763071 GTGTTCTTTCTATTCCCACGTTATAGT 59.237 37.037 0.00 0.00 0.00 2.12
646 653 9.978044 GTTCTTTCTATTCCCACGTTATAGTAT 57.022 33.333 0.00 0.00 0.00 2.12
689 707 2.225727 CCAAGGCCAAAGAACGAAGTAC 59.774 50.000 5.01 0.00 45.00 2.73
690 708 3.139077 CAAGGCCAAAGAACGAAGTACT 58.861 45.455 5.01 0.00 45.00 2.73
691 709 3.041508 AGGCCAAAGAACGAAGTACTC 57.958 47.619 5.01 0.00 45.00 2.59
692 710 2.633481 AGGCCAAAGAACGAAGTACTCT 59.367 45.455 5.01 0.00 45.00 3.24
693 711 3.830755 AGGCCAAAGAACGAAGTACTCTA 59.169 43.478 5.01 0.00 45.00 2.43
696 714 4.858140 GCCAAAGAACGAAGTACTCTAGAC 59.142 45.833 0.00 0.00 45.00 2.59
699 717 3.598299 AGAACGAAGTACTCTAGACGCT 58.402 45.455 0.00 0.00 45.00 5.07
752 770 5.529800 ACTGTACACATAGCCGAAAAACTTT 59.470 36.000 0.00 0.00 0.00 2.66
753 771 5.753744 TGTACACATAGCCGAAAAACTTTG 58.246 37.500 0.00 0.00 0.00 2.77
754 772 4.911514 ACACATAGCCGAAAAACTTTGT 57.088 36.364 0.00 0.00 0.00 2.83
755 773 4.855531 ACACATAGCCGAAAAACTTTGTC 58.144 39.130 0.00 0.00 0.00 3.18
756 774 4.336993 ACACATAGCCGAAAAACTTTGTCA 59.663 37.500 0.00 0.00 0.00 3.58
758 776 5.920273 CACATAGCCGAAAAACTTTGTCATT 59.080 36.000 0.00 0.00 0.00 2.57
759 777 7.081349 CACATAGCCGAAAAACTTTGTCATTA 58.919 34.615 0.00 0.00 0.00 1.90
760 778 7.593273 CACATAGCCGAAAAACTTTGTCATTAA 59.407 33.333 0.00 0.00 0.00 1.40
761 779 8.303876 ACATAGCCGAAAAACTTTGTCATTAAT 58.696 29.630 0.00 0.00 0.00 1.40
762 780 9.781834 CATAGCCGAAAAACTTTGTCATTAATA 57.218 29.630 0.00 0.00 0.00 0.98
802 2283 6.346477 ACAATATATCGGTCTACACATGCT 57.654 37.500 0.00 0.00 0.00 3.79
804 2285 6.868864 ACAATATATCGGTCTACACATGCTTC 59.131 38.462 0.00 0.00 0.00 3.86
826 2307 2.325761 CAAAGCACATCTTGAAGCTGC 58.674 47.619 0.00 0.00 33.97 5.25
849 2358 0.824759 ACTGCCGTATCTCCAACTCC 59.175 55.000 0.00 0.00 0.00 3.85
854 2363 1.202463 CCGTATCTCCAACTCCAGCTG 60.202 57.143 6.78 6.78 0.00 4.24
872 2381 2.551459 GCTGCAGTGGCCTAAAGATATG 59.449 50.000 16.64 0.00 40.13 1.78
885 2399 6.317391 GCCTAAAGATATGCAAAGTCAGAGTT 59.683 38.462 0.00 0.00 0.00 3.01
935 2456 4.376223 TCCCACCATCCAAGGTAGAATAA 58.624 43.478 0.00 0.00 40.77 1.40
940 2461 4.163458 ACCATCCAAGGTAGAATAAAGCGA 59.837 41.667 0.00 0.00 40.98 4.93
947 2468 5.099042 AGGTAGAATAAAGCGACCACAAT 57.901 39.130 0.00 0.00 34.00 2.71
956 2477 0.951558 GCGACCACAATCCACACTTT 59.048 50.000 0.00 0.00 0.00 2.66
957 2478 1.336755 GCGACCACAATCCACACTTTT 59.663 47.619 0.00 0.00 0.00 2.27
958 2479 2.223711 GCGACCACAATCCACACTTTTT 60.224 45.455 0.00 0.00 0.00 1.94
981 2502 6.474140 TTTTCTCAAAAAGGAGTTTACCCC 57.526 37.500 0.00 0.00 36.30 4.95
982 2503 4.799715 TCTCAAAAAGGAGTTTACCCCA 57.200 40.909 0.00 0.00 36.30 4.96
983 2504 4.725490 TCTCAAAAAGGAGTTTACCCCAG 58.275 43.478 0.00 0.00 36.30 4.45
984 2505 3.227614 TCAAAAAGGAGTTTACCCCAGC 58.772 45.455 0.00 0.00 0.00 4.85
985 2506 2.299013 CAAAAAGGAGTTTACCCCAGCC 59.701 50.000 0.00 0.00 0.00 4.85
986 2507 1.456919 AAAGGAGTTTACCCCAGCCT 58.543 50.000 0.00 0.00 0.00 4.58
987 2508 1.456919 AAGGAGTTTACCCCAGCCTT 58.543 50.000 0.00 0.00 0.00 4.35
988 2509 1.456919 AGGAGTTTACCCCAGCCTTT 58.543 50.000 0.00 0.00 0.00 3.11
989 2510 2.639487 AGGAGTTTACCCCAGCCTTTA 58.361 47.619 0.00 0.00 0.00 1.85
990 2511 2.307980 AGGAGTTTACCCCAGCCTTTAC 59.692 50.000 0.00 0.00 0.00 2.01
991 2512 2.040679 GGAGTTTACCCCAGCCTTTACA 59.959 50.000 0.00 0.00 0.00 2.41
992 2513 3.308904 GGAGTTTACCCCAGCCTTTACAT 60.309 47.826 0.00 0.00 0.00 2.29
993 2514 3.945921 GAGTTTACCCCAGCCTTTACATC 59.054 47.826 0.00 0.00 0.00 3.06
994 2515 3.332485 AGTTTACCCCAGCCTTTACATCA 59.668 43.478 0.00 0.00 0.00 3.07
995 2516 3.644966 TTACCCCAGCCTTTACATCAG 57.355 47.619 0.00 0.00 0.00 2.90
996 2517 1.668826 ACCCCAGCCTTTACATCAGA 58.331 50.000 0.00 0.00 0.00 3.27
997 2518 1.992557 ACCCCAGCCTTTACATCAGAA 59.007 47.619 0.00 0.00 0.00 3.02
998 2519 2.378547 ACCCCAGCCTTTACATCAGAAA 59.621 45.455 0.00 0.00 0.00 2.52
999 2520 3.019564 CCCCAGCCTTTACATCAGAAAG 58.980 50.000 0.00 0.00 34.32 2.62
1000 2521 3.308402 CCCCAGCCTTTACATCAGAAAGA 60.308 47.826 0.00 0.00 36.22 2.52
1001 2522 4.530875 CCCAGCCTTTACATCAGAAAGAT 58.469 43.478 0.00 0.00 36.22 2.40
1012 2533 5.573296 CATCAGAAAGATGCATACGACTC 57.427 43.478 0.00 0.00 46.90 3.36
1013 2534 4.718940 TCAGAAAGATGCATACGACTCA 57.281 40.909 0.00 0.00 0.00 3.41
1014 2535 5.268118 TCAGAAAGATGCATACGACTCAT 57.732 39.130 0.00 0.00 0.00 2.90
1015 2536 6.391227 TCAGAAAGATGCATACGACTCATA 57.609 37.500 0.00 0.00 0.00 2.15
1016 2537 6.986250 TCAGAAAGATGCATACGACTCATAT 58.014 36.000 0.00 0.00 0.00 1.78
1017 2538 7.436933 TCAGAAAGATGCATACGACTCATATT 58.563 34.615 0.00 0.00 0.00 1.28
1018 2539 8.576442 TCAGAAAGATGCATACGACTCATATTA 58.424 33.333 0.00 0.00 0.00 0.98
1019 2540 9.363763 CAGAAAGATGCATACGACTCATATTAT 57.636 33.333 0.00 0.00 0.00 1.28
1020 2541 9.935241 AGAAAGATGCATACGACTCATATTATT 57.065 29.630 0.00 0.00 0.00 1.40
1040 2561 5.914898 ATTAAAAAGATACCACAGCCCAC 57.085 39.130 0.00 0.00 0.00 4.61
1045 2566 1.003580 AGATACCACAGCCCACACTTG 59.996 52.381 0.00 0.00 0.00 3.16
1089 2610 2.086054 AGAACACTCTCCAATGCGTC 57.914 50.000 0.00 0.00 0.00 5.19
1596 3117 3.188786 GAGCACGGCATGTCGGTC 61.189 66.667 25.37 14.67 0.00 4.79
1734 3255 1.149174 CGCCATGGGTAAGATGCCT 59.851 57.895 15.13 0.00 0.00 4.75
2283 3804 1.303888 CCTGTGCCTTGCCATGAGT 60.304 57.895 0.00 0.00 0.00 3.41
2427 4538 3.100658 TGAACTGAATGAACGAACCGA 57.899 42.857 0.00 0.00 0.00 4.69
2485 4799 8.402798 TGCTTGTAAACTCCATTGAATAAAGA 57.597 30.769 0.00 0.00 0.00 2.52
2520 4834 2.238646 TCCAGAATCCACCATTACGCTT 59.761 45.455 0.00 0.00 0.00 4.68
2626 4940 1.518929 CTCGTCCGAATGAGCGATTTC 59.481 52.381 0.00 0.00 31.96 2.17
2677 4994 1.403249 GCAATTCAGTCATGGTGCCAC 60.403 52.381 0.00 0.00 0.00 5.01
2678 4995 1.887854 CAATTCAGTCATGGTGCCACA 59.112 47.619 0.00 0.00 0.00 4.17
2679 4996 1.538047 ATTCAGTCATGGTGCCACAC 58.462 50.000 0.00 0.00 0.00 3.82
2680 4997 0.473755 TTCAGTCATGGTGCCACACT 59.526 50.000 0.00 0.00 34.40 3.55
2681 4998 0.250424 TCAGTCATGGTGCCACACTG 60.250 55.000 18.98 18.98 39.60 3.66
2682 4999 1.601759 AGTCATGGTGCCACACTGC 60.602 57.895 0.00 0.00 34.40 4.40
2683 5000 2.282391 TCATGGTGCCACACTGCC 60.282 61.111 0.00 0.00 34.40 4.85
2684 5001 2.598099 CATGGTGCCACACTGCCA 60.598 61.111 0.00 0.00 34.40 4.92
2735 5070 3.869272 GCTCGCCATGAACAGCCG 61.869 66.667 0.00 0.00 0.00 5.52
2736 5071 3.197790 CTCGCCATGAACAGCCGG 61.198 66.667 0.00 0.00 0.00 6.13
2737 5072 4.776322 TCGCCATGAACAGCCGGG 62.776 66.667 2.18 0.00 0.00 5.73
2770 5105 2.358737 GCGTGAAGGGGTGACAGG 60.359 66.667 0.00 0.00 0.00 4.00
2864 5199 0.976073 TGCTACTGTAGGCTCCCCAC 60.976 60.000 16.09 0.00 0.00 4.61
2870 5205 2.443390 TAGGCTCCCCACGCTACC 60.443 66.667 0.00 0.00 0.00 3.18
2901 5237 6.834969 TCCAAATCTCCATATGATTCAGCAAA 59.165 34.615 3.65 0.00 33.54 3.68
2904 5240 5.378230 TCTCCATATGATTCAGCAAAGGT 57.622 39.130 3.65 0.00 0.00 3.50
2905 5241 5.128205 TCTCCATATGATTCAGCAAAGGTG 58.872 41.667 3.65 0.00 0.00 4.00
2908 5244 2.226962 ATGATTCAGCAAAGGTGGCT 57.773 45.000 0.00 0.00 43.77 4.75
2924 5260 2.105128 CTCGCCCTACCGCAAGAG 59.895 66.667 0.00 0.00 43.02 2.85
2995 5331 1.447140 GACCGCAACGCCAGTGATA 60.447 57.895 0.00 0.00 0.00 2.15
2998 5334 1.134640 ACCGCAACGCCAGTGATATTA 60.135 47.619 0.00 0.00 0.00 0.98
2999 5335 2.143122 CCGCAACGCCAGTGATATTAT 58.857 47.619 0.00 0.00 0.00 1.28
3035 5371 3.558033 ACATGGATGATGTTGCATAGCA 58.442 40.909 0.00 0.00 43.20 3.49
3064 5400 3.488384 GCAACAAGGACGACATTTCAACA 60.488 43.478 0.00 0.00 0.00 3.33
3069 5405 1.804748 GGACGACATTTCAACAGGTCC 59.195 52.381 0.00 0.00 36.11 4.46
3073 5409 2.500229 GACATTTCAACAGGTCCCGAA 58.500 47.619 0.00 0.00 0.00 4.30
3084 5420 3.326880 ACAGGTCCCGAAAACTTCTACAT 59.673 43.478 0.00 0.00 0.00 2.29
3100 5436 1.175654 ACATGGATGATGTTGCGCAA 58.824 45.000 21.02 21.02 43.20 4.85
3114 5450 2.572812 GCAATGGCGAATGCACCA 59.427 55.556 3.63 0.00 45.35 4.17
3115 5451 1.517694 GCAATGGCGAATGCACCAG 60.518 57.895 3.63 0.00 45.35 4.00
3167 5505 1.576421 GCAAAGACGGCTCCAACAG 59.424 57.895 0.00 0.00 0.00 3.16
3197 5535 0.447801 GCAATGGCAACGACTACAGG 59.552 55.000 0.00 0.00 40.72 4.00
3201 5539 2.345991 GCAACGACTACAGGGGCA 59.654 61.111 0.00 0.00 0.00 5.36
3243 5581 1.078709 CACGATGGCGAAGATGTTGT 58.921 50.000 0.00 0.00 41.64 3.32
3287 5625 1.403972 GACGACGTGCTTCGCCTAAG 61.404 60.000 4.58 0.00 43.06 2.18
3302 5640 3.751698 CGCCTAAGCCAGGGAATATTTAC 59.248 47.826 4.23 0.00 45.66 2.01
3315 5653 8.624776 CAGGGAATATTTACTCAAAGTCCATTC 58.375 37.037 0.00 0.00 30.18 2.67
3369 5707 1.344763 AGTTGTGTCCCACTACTCAGC 59.655 52.381 5.79 0.00 44.27 4.26
3373 5711 2.438021 TGTGTCCCACTACTCAGCTTTT 59.562 45.455 0.00 0.00 35.11 2.27
3374 5712 3.067833 GTGTCCCACTACTCAGCTTTTC 58.932 50.000 0.00 0.00 0.00 2.29
3375 5713 2.038557 TGTCCCACTACTCAGCTTTTCC 59.961 50.000 0.00 0.00 0.00 3.13
3388 5726 7.224297 ACTCAGCTTTTCCATTAGAAGTTACA 58.776 34.615 0.00 0.00 35.40 2.41
3389 5727 7.719633 ACTCAGCTTTTCCATTAGAAGTTACAA 59.280 33.333 0.00 0.00 35.40 2.41
3390 5728 7.871853 TCAGCTTTTCCATTAGAAGTTACAAC 58.128 34.615 0.00 0.00 35.40 3.32
3391 5729 7.719633 TCAGCTTTTCCATTAGAAGTTACAACT 59.280 33.333 0.00 0.00 42.04 3.16
3392 5730 8.999431 CAGCTTTTCCATTAGAAGTTACAACTA 58.001 33.333 0.00 0.00 38.57 2.24
3393 5731 9.740710 AGCTTTTCCATTAGAAGTTACAACTAT 57.259 29.630 0.00 0.00 38.57 2.12
3399 5737 9.613428 TCCATTAGAAGTTACAACTATTCCATG 57.387 33.333 0.00 0.00 38.57 3.66
3400 5738 9.613428 CCATTAGAAGTTACAACTATTCCATGA 57.387 33.333 0.00 0.00 38.57 3.07
3404 5742 8.954950 AGAAGTTACAACTATTCCATGAGATG 57.045 34.615 0.00 0.00 38.57 2.90
3405 5743 7.497249 AGAAGTTACAACTATTCCATGAGATGC 59.503 37.037 0.00 0.00 38.57 3.91
3406 5744 6.653020 AGTTACAACTATTCCATGAGATGCA 58.347 36.000 0.00 0.00 37.52 3.96
3407 5745 7.285566 AGTTACAACTATTCCATGAGATGCAT 58.714 34.615 0.00 0.00 37.52 3.96
3408 5746 7.228108 AGTTACAACTATTCCATGAGATGCATG 59.772 37.037 2.46 0.00 44.58 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.645058 ATTTTTATCACCATAACCAGGAGTG 57.355 36.000 0.00 0.00 0.00 3.51
34 35 8.135529 GTGCCTCTTATTTTTATCACCATAACC 58.864 37.037 0.00 0.00 0.00 2.85
60 61 1.002087 AGACCCTAGCTTGGTTTCACG 59.998 52.381 13.38 0.00 35.85 4.35
103 104 5.412640 TGAACCGAATTTATCTTAGTGCGA 58.587 37.500 0.00 0.00 0.00 5.10
117 118 0.038166 ATGGTGCCACTGAACCGAAT 59.962 50.000 0.00 0.00 39.47 3.34
121 122 0.250901 AGTCATGGTGCCACTGAACC 60.251 55.000 0.00 0.00 36.96 3.62
125 126 0.877071 GTCAAGTCATGGTGCCACTG 59.123 55.000 0.00 0.00 0.00 3.66
126 127 0.250901 GGTCAAGTCATGGTGCCACT 60.251 55.000 0.00 0.00 0.00 4.00
158 159 5.048846 ACATGAACCTGTTTAGTCAACCT 57.951 39.130 0.00 0.00 33.97 3.50
162 163 7.220740 TGAACATACATGAACCTGTTTAGTCA 58.779 34.615 0.00 0.00 32.28 3.41
172 176 3.505680 TGCCACTTGAACATACATGAACC 59.494 43.478 0.00 0.00 0.00 3.62
229 233 1.680989 GGTGGGGTATGGTTGCCAC 60.681 63.158 0.00 0.00 35.80 5.01
230 234 2.767352 GGTGGGGTATGGTTGCCA 59.233 61.111 0.00 0.00 38.19 4.92
275 279 4.401519 CCGACTTTATCTCCTTGTAGACCA 59.598 45.833 0.00 0.00 0.00 4.02
281 285 5.952347 ATAACCCGACTTTATCTCCTTGT 57.048 39.130 0.00 0.00 0.00 3.16
295 299 3.054287 TGCAACCAATCCTTATAACCCGA 60.054 43.478 0.00 0.00 0.00 5.14
689 707 1.531149 GCTCTGCTCTAGCGTCTAGAG 59.469 57.143 26.37 26.37 45.83 2.43
690 708 1.588674 GCTCTGCTCTAGCGTCTAGA 58.411 55.000 13.54 13.54 45.83 2.43
699 717 3.518998 GCCGTCCGCTCTGCTCTA 61.519 66.667 0.00 0.00 0.00 2.43
785 2266 3.349488 CGAAGCATGTGTAGACCGATA 57.651 47.619 0.00 0.00 0.00 2.92
802 2283 2.605338 GCTTCAAGATGTGCTTTGCGAA 60.605 45.455 0.00 0.00 33.60 4.70
804 2285 1.068748 AGCTTCAAGATGTGCTTTGCG 60.069 47.619 0.00 0.00 33.60 4.85
811 2292 3.124806 CAGTACAGCAGCTTCAAGATGTG 59.875 47.826 4.24 4.31 33.43 3.21
819 2300 0.108804 TACGGCAGTACAGCAGCTTC 60.109 55.000 12.66 0.00 35.83 3.86
826 2307 2.427453 AGTTGGAGATACGGCAGTACAG 59.573 50.000 0.00 0.00 35.39 2.74
849 2358 0.321919 TCTTTAGGCCACTGCAGCTG 60.322 55.000 15.27 10.11 40.13 4.24
854 2363 2.575532 TGCATATCTTTAGGCCACTGC 58.424 47.619 5.01 2.22 34.24 4.40
872 2381 4.377841 GCACATCTACAACTCTGACTTTGC 60.378 45.833 0.00 0.00 0.00 3.68
915 2429 4.580580 GCTTTATTCTACCTTGGATGGTGG 59.419 45.833 0.00 0.00 41.05 4.61
916 2430 4.273480 CGCTTTATTCTACCTTGGATGGTG 59.727 45.833 0.00 0.00 41.05 4.17
924 2445 4.546829 TGTGGTCGCTTTATTCTACCTT 57.453 40.909 0.00 0.00 0.00 3.50
935 2456 0.108585 AGTGTGGATTGTGGTCGCTT 59.891 50.000 0.00 0.00 0.00 4.68
957 2478 6.440965 TGGGGTAAACTCCTTTTTGAGAAAAA 59.559 34.615 0.00 0.00 37.99 1.94
958 2479 5.958987 TGGGGTAAACTCCTTTTTGAGAAAA 59.041 36.000 0.00 0.00 36.22 2.29
959 2480 5.520751 TGGGGTAAACTCCTTTTTGAGAAA 58.479 37.500 0.00 0.00 36.22 2.52
960 2481 5.132043 TGGGGTAAACTCCTTTTTGAGAA 57.868 39.130 0.00 0.00 36.22 2.87
961 2482 4.725490 CTGGGGTAAACTCCTTTTTGAGA 58.275 43.478 0.00 0.00 36.22 3.27
962 2483 3.255888 GCTGGGGTAAACTCCTTTTTGAG 59.744 47.826 0.00 0.00 38.37 3.02
963 2484 3.227614 GCTGGGGTAAACTCCTTTTTGA 58.772 45.455 0.00 0.00 0.00 2.69
964 2485 2.299013 GGCTGGGGTAAACTCCTTTTTG 59.701 50.000 0.00 0.00 0.00 2.44
965 2486 2.179204 AGGCTGGGGTAAACTCCTTTTT 59.821 45.455 0.00 0.00 0.00 1.94
966 2487 1.787058 AGGCTGGGGTAAACTCCTTTT 59.213 47.619 0.00 0.00 0.00 2.27
967 2488 1.456919 AGGCTGGGGTAAACTCCTTT 58.543 50.000 0.00 0.00 0.00 3.11
968 2489 1.456919 AAGGCTGGGGTAAACTCCTT 58.543 50.000 0.00 0.00 0.00 3.36
969 2490 1.456919 AAAGGCTGGGGTAAACTCCT 58.543 50.000 0.00 0.00 0.00 3.69
970 2491 2.040679 TGTAAAGGCTGGGGTAAACTCC 59.959 50.000 0.00 0.00 0.00 3.85
971 2492 3.428413 TGTAAAGGCTGGGGTAAACTC 57.572 47.619 0.00 0.00 0.00 3.01
972 2493 3.332485 TGATGTAAAGGCTGGGGTAAACT 59.668 43.478 0.00 0.00 0.00 2.66
973 2494 3.692690 TGATGTAAAGGCTGGGGTAAAC 58.307 45.455 0.00 0.00 0.00 2.01
974 2495 3.589735 TCTGATGTAAAGGCTGGGGTAAA 59.410 43.478 0.00 0.00 0.00 2.01
975 2496 3.186283 TCTGATGTAAAGGCTGGGGTAA 58.814 45.455 0.00 0.00 0.00 2.85
976 2497 2.840511 TCTGATGTAAAGGCTGGGGTA 58.159 47.619 0.00 0.00 0.00 3.69
977 2498 1.668826 TCTGATGTAAAGGCTGGGGT 58.331 50.000 0.00 0.00 0.00 4.95
978 2499 2.806945 TTCTGATGTAAAGGCTGGGG 57.193 50.000 0.00 0.00 0.00 4.96
979 2500 3.955471 TCTTTCTGATGTAAAGGCTGGG 58.045 45.455 0.00 0.00 35.18 4.45
980 2501 5.496133 CATCTTTCTGATGTAAAGGCTGG 57.504 43.478 0.00 0.00 45.55 4.85
991 2512 5.268118 TGAGTCGTATGCATCTTTCTGAT 57.732 39.130 0.19 0.00 35.40 2.90
992 2513 4.718940 TGAGTCGTATGCATCTTTCTGA 57.281 40.909 0.19 0.00 0.00 3.27
993 2514 7.649370 AATATGAGTCGTATGCATCTTTCTG 57.351 36.000 0.19 0.00 0.00 3.02
994 2515 9.935241 AATAATATGAGTCGTATGCATCTTTCT 57.065 29.630 0.19 0.00 0.00 2.52
1013 2534 9.875708 TGGGCTGTGGTATCTTTTTAATAATAT 57.124 29.630 0.00 0.00 0.00 1.28
1014 2535 9.127277 GTGGGCTGTGGTATCTTTTTAATAATA 57.873 33.333 0.00 0.00 0.00 0.98
1015 2536 7.617723 TGTGGGCTGTGGTATCTTTTTAATAAT 59.382 33.333 0.00 0.00 0.00 1.28
1016 2537 6.948886 TGTGGGCTGTGGTATCTTTTTAATAA 59.051 34.615 0.00 0.00 0.00 1.40
1017 2538 6.376018 GTGTGGGCTGTGGTATCTTTTTAATA 59.624 38.462 0.00 0.00 0.00 0.98
1018 2539 5.185056 GTGTGGGCTGTGGTATCTTTTTAAT 59.815 40.000 0.00 0.00 0.00 1.40
1019 2540 4.521256 GTGTGGGCTGTGGTATCTTTTTAA 59.479 41.667 0.00 0.00 0.00 1.52
1020 2541 4.076394 GTGTGGGCTGTGGTATCTTTTTA 58.924 43.478 0.00 0.00 0.00 1.52
1021 2542 2.890945 GTGTGGGCTGTGGTATCTTTTT 59.109 45.455 0.00 0.00 0.00 1.94
1022 2543 2.108250 AGTGTGGGCTGTGGTATCTTTT 59.892 45.455 0.00 0.00 0.00 2.27
1023 2544 1.705186 AGTGTGGGCTGTGGTATCTTT 59.295 47.619 0.00 0.00 0.00 2.52
1024 2545 1.362224 AGTGTGGGCTGTGGTATCTT 58.638 50.000 0.00 0.00 0.00 2.40
1025 2546 1.003580 CAAGTGTGGGCTGTGGTATCT 59.996 52.381 0.00 0.00 0.00 1.98
1026 2547 1.453155 CAAGTGTGGGCTGTGGTATC 58.547 55.000 0.00 0.00 0.00 2.24
1027 2548 0.038166 CCAAGTGTGGGCTGTGGTAT 59.962 55.000 0.00 0.00 41.77 2.73
1028 2549 1.454104 CCAAGTGTGGGCTGTGGTA 59.546 57.895 0.00 0.00 41.77 3.25
1040 2561 3.027170 GCCATCGACGTGCCAAGTG 62.027 63.158 0.00 0.00 0.00 3.16
1045 2566 3.576356 CATGGCCATCGACGTGCC 61.576 66.667 17.61 13.29 45.56 5.01
1050 2571 2.281070 ATCGCCATGGCCATCGAC 60.281 61.111 30.79 13.94 37.98 4.20
1089 2610 2.434884 AGCGCCATCAGGAACACG 60.435 61.111 2.29 0.00 36.89 4.49
1203 2724 3.025619 GCATAGTCATGGTGCGCC 58.974 61.111 10.11 10.11 32.36 6.53
1206 2727 1.645455 CAGCGCATAGTCATGGTGC 59.355 57.895 11.47 0.00 38.28 5.01
1378 2899 1.891060 GCGTCGAGCTTGAGGTTGTG 61.891 60.000 21.67 3.02 44.04 3.33
1734 3255 1.433471 CTGCATGACGAGCGAGGTA 59.567 57.895 0.00 0.00 33.85 3.08
2427 4538 0.478072 TCCATGGGAAGCACTGTTGT 59.522 50.000 13.02 0.00 0.00 3.32
2485 4799 2.839486 TCTGGATTGTGAGCGTTTCT 57.161 45.000 0.00 0.00 0.00 2.52
2626 4940 1.219935 CGTTTAGGGAGGAACGGGG 59.780 63.158 1.06 0.00 43.44 5.73
2663 4980 1.859427 GCAGTGTGGCACCATGACTG 61.859 60.000 23.90 23.90 39.86 3.51
2735 5070 1.374758 CAACAGTGTCGCCTCTCCC 60.375 63.158 0.00 0.00 0.00 4.30
2736 5071 2.029844 GCAACAGTGTCGCCTCTCC 61.030 63.158 0.00 0.00 0.00 3.71
2737 5072 2.375766 CGCAACAGTGTCGCCTCTC 61.376 63.158 0.00 0.00 0.00 3.20
2770 5105 4.314440 TCCCGACAGCTGTGGTGC 62.314 66.667 27.27 8.82 34.04 5.01
2790 5125 3.437795 CCGGGAGCAGTCGTACGT 61.438 66.667 16.05 0.00 0.00 3.57
2791 5126 4.849329 GCCGGGAGCAGTCGTACG 62.849 72.222 9.53 9.53 42.97 3.67
2792 5127 4.849329 CGCCGGGAGCAGTCGTAC 62.849 72.222 2.18 0.00 44.04 3.67
2864 5199 1.065418 AGATTTGGACCCTTGGTAGCG 60.065 52.381 0.00 0.00 35.25 4.26
2870 5205 5.052693 TCATATGGAGATTTGGACCCTTG 57.947 43.478 2.13 0.00 0.00 3.61
2908 5244 1.378911 TACTCTTGCGGTAGGGCGA 60.379 57.895 0.00 0.00 35.06 5.54
2924 5260 2.025727 CGACGGGGACATCGCTAC 59.974 66.667 0.00 0.00 32.15 3.58
2974 5310 3.276846 ACTGGCGTTGCGGTCAAC 61.277 61.111 5.56 5.56 46.85 3.18
2989 5325 4.795268 CACGACGCCACTATAATATCACT 58.205 43.478 0.00 0.00 0.00 3.41
2995 5331 1.931172 GTTGCACGACGCCACTATAAT 59.069 47.619 0.00 0.00 41.33 1.28
2998 5334 0.391130 ATGTTGCACGACGCCACTAT 60.391 50.000 0.00 0.00 41.33 2.12
2999 5335 1.005512 ATGTTGCACGACGCCACTA 60.006 52.632 0.00 0.00 41.33 2.74
3035 5371 0.602638 TCGTCCTTGTTGCATTCGCT 60.603 50.000 0.00 0.00 39.64 4.93
3047 5383 3.139077 GACCTGTTGAAATGTCGTCCTT 58.861 45.455 0.00 0.00 0.00 3.36
3064 5400 3.307480 CCATGTAGAAGTTTTCGGGACCT 60.307 47.826 0.00 0.00 34.02 3.85
3069 5405 5.586243 ACATCATCCATGTAGAAGTTTTCGG 59.414 40.000 0.00 0.00 44.56 4.30
3073 5409 5.163723 CGCAACATCATCCATGTAGAAGTTT 60.164 40.000 0.00 0.00 45.77 2.66
3084 5420 0.456628 CCATTGCGCAACATCATCCA 59.543 50.000 27.64 0.00 0.00 3.41
3112 5448 2.664851 TTTCAGTGTCGCCGCTGG 60.665 61.111 7.22 0.00 46.88 4.85
3114 5450 1.222115 GAACTTTCAGTGTCGCCGCT 61.222 55.000 0.00 0.00 0.00 5.52
3115 5451 1.204312 GAACTTTCAGTGTCGCCGC 59.796 57.895 0.00 0.00 0.00 6.53
3118 5454 1.205657 TGTCGAACTTTCAGTGTCGC 58.794 50.000 0.00 0.00 32.69 5.19
3119 5455 3.787826 CATTGTCGAACTTTCAGTGTCG 58.212 45.455 0.00 0.00 33.37 4.35
3153 5491 0.036952 CATGTCTGTTGGAGCCGTCT 60.037 55.000 0.00 0.00 0.00 4.18
3158 5496 1.267806 CAACACCATGTCTGTTGGAGC 59.732 52.381 19.13 0.00 43.21 4.70
3167 5505 0.317799 TGCCATTGCAACACCATGTC 59.682 50.000 0.00 0.00 46.66 3.06
3197 5535 1.940752 GCCATCACAACATTGTTGCCC 60.941 52.381 25.60 7.44 39.91 5.36
3201 5539 1.952990 TGTCGCCATCACAACATTGTT 59.047 42.857 0.00 0.00 39.91 2.83
3229 5567 1.452110 CCATCACAACATCTTCGCCA 58.548 50.000 0.00 0.00 0.00 5.69
3234 5572 1.078709 CGTCGCCATCACAACATCTT 58.921 50.000 0.00 0.00 0.00 2.40
3287 5625 5.299531 GGACTTTGAGTAAATATTCCCTGGC 59.700 44.000 0.00 0.00 0.00 4.85
3358 5696 5.734720 TCTAATGGAAAAGCTGAGTAGTGG 58.265 41.667 0.00 0.00 0.00 4.00
3373 5711 9.613428 CATGGAATAGTTGTAACTTCTAATGGA 57.387 33.333 2.20 0.00 40.37 3.41
3374 5712 9.613428 TCATGGAATAGTTGTAACTTCTAATGG 57.387 33.333 2.20 0.00 40.37 3.16


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

AutoCloner maintained by Alex Coulton.