Multiple sequence alignment - TraesCS5D01G417000

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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 TraesCS5D01G417000 chr5D 100.000 3216 0 0 1 3216 479157419 479154204 0.000000e+00 5939
1 TraesCS5D01G417000 chr5B 89.628 2632 180 52 489 3058 586876969 586874369 0.000000e+00 3262
2 TraesCS5D01G417000 chr5B 92.405 79 6 0 393 471 586877621 586877543 2.620000e-21 113
3 TraesCS5D01G417000 chr5A 88.906 2605 168 52 395 2932 597850920 597848370 0.000000e+00 3097
4 TraesCS5D01G417000 chr5A 93.434 396 25 1 2 396 597851439 597851044 1.290000e-163 586
5 TraesCS5D01G417000 chr5A 78.766 843 113 35 1296 2089 415195433 415194608 3.700000e-139 505
6 TraesCS5D01G417000 chr3B 80.284 1055 134 40 1296 2293 800996768 800997805 0.000000e+00 728
7 TraesCS5D01G417000 chr6D 78.892 1047 155 39 1296 2293 306002807 306003836 0.000000e+00 649
8 TraesCS5D01G417000 chr2A 79.323 827 117 31 1296 2083 6126454 6127265 6.110000e-147 531
9 TraesCS5D01G417000 chr2A 79.202 827 118 31 1296 2083 6177493 6178304 2.840000e-145 525
10 TraesCS5D01G417000 chr2A 78.476 827 124 33 1296 2083 6073685 6074496 2.880000e-135 492
11 TraesCS5D01G417000 chr2A 77.679 560 70 36 992 1544 459446356 459446867 1.130000e-74 291
12 TraesCS5D01G417000 chr2A 77.500 560 70 42 992 1544 459507477 459507987 5.250000e-73 285
13 TraesCS5D01G417000 chr2A 77.658 555 59 50 992 1534 459545274 459545775 8.790000e-71 278
14 TraesCS5D01G417000 chr2A 84.800 125 12 7 116 238 73184292 73184411 5.640000e-23 119
15 TraesCS5D01G417000 chr3D 78.673 844 115 37 1296 2089 126612539 126611711 4.790000e-138 501
16 TraesCS5D01G417000 chr3D 84.848 132 16 3 371 499 596210399 596210529 2.600000e-26 130
17 TraesCS5D01G417000 chr6B 79.676 679 96 21 1653 2293 148829148 148829822 4.890000e-123 451
18 TraesCS5D01G417000 chr6B 83.399 253 30 8 1296 1546 148828697 148828939 1.160000e-54 224
19 TraesCS5D01G417000 chr6B 85.833 120 17 0 2174 2293 11708839 11708720 9.360000e-26 128


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 TraesCS5D01G417000 chr5D 479154204 479157419 3215 True 5939.0 5939 100.0000 1 3216 1 chr5D.!!$R1 3215
1 TraesCS5D01G417000 chr5B 586874369 586877621 3252 True 1687.5 3262 91.0165 393 3058 2 chr5B.!!$R1 2665
2 TraesCS5D01G417000 chr5A 597848370 597851439 3069 True 1841.5 3097 91.1700 2 2932 2 chr5A.!!$R2 2930
3 TraesCS5D01G417000 chr5A 415194608 415195433 825 True 505.0 505 78.7660 1296 2089 1 chr5A.!!$R1 793
4 TraesCS5D01G417000 chr3B 800996768 800997805 1037 False 728.0 728 80.2840 1296 2293 1 chr3B.!!$F1 997
5 TraesCS5D01G417000 chr6D 306002807 306003836 1029 False 649.0 649 78.8920 1296 2293 1 chr6D.!!$F1 997
6 TraesCS5D01G417000 chr2A 6126454 6127265 811 False 531.0 531 79.3230 1296 2083 1 chr2A.!!$F2 787
7 TraesCS5D01G417000 chr2A 6177493 6178304 811 False 525.0 525 79.2020 1296 2083 1 chr2A.!!$F3 787
8 TraesCS5D01G417000 chr2A 6073685 6074496 811 False 492.0 492 78.4760 1296 2083 1 chr2A.!!$F1 787
9 TraesCS5D01G417000 chr2A 459446356 459446867 511 False 291.0 291 77.6790 992 1544 1 chr2A.!!$F5 552
10 TraesCS5D01G417000 chr2A 459507477 459507987 510 False 285.0 285 77.5000 992 1544 1 chr2A.!!$F6 552
11 TraesCS5D01G417000 chr2A 459545274 459545775 501 False 278.0 278 77.6580 992 1534 1 chr2A.!!$F7 542
12 TraesCS5D01G417000 chr3D 126611711 126612539 828 True 501.0 501 78.6730 1296 2089 1 chr3D.!!$R1 793
13 TraesCS5D01G417000 chr6B 148828697 148829822 1125 False 337.5 451 81.5375 1296 2293 2 chr6B.!!$F1 997

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
45 46 0.179048 TATGGCGAGGGCATTCACAG 60.179 55.0 10.00 0.0 46.61 3.66 F
1178 1868 0.530650 CTGTAGATCCGTGGCGCAAT 60.531 55.0 10.83 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 2076 0.583438 CGCATACCTTGATGAAGCCG 59.417 55.0 0.00 0.00 0.0 5.52 R
2836 3753 0.035439 AATTGTTGGCCTCCGACGAT 60.035 50.0 3.32 0.14 42.3 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
21 22 2.097466 CGGCTATTGCGGTCTTCAAAAT 59.903 45.455 0.00 0.00 40.82 1.82
45 46 0.179048 TATGGCGAGGGCATTCACAG 60.179 55.000 10.00 0.00 46.61 3.66
62 63 4.170256 TCACAGGTTTCGTTTTTCTTTGC 58.830 39.130 0.00 0.00 0.00 3.68
88 89 8.918202 TGTTGGTTCAGTGTAATTCTTAATCT 57.082 30.769 0.00 0.00 0.00 2.40
99 100 1.595382 CTTAATCTCTGGCCGGCGG 60.595 63.158 24.35 24.35 0.00 6.13
100 101 2.311688 CTTAATCTCTGGCCGGCGGT 62.312 60.000 28.82 7.28 0.00 5.68
110 111 2.036006 GCCGGCGGTGTACAATCAA 61.036 57.895 28.82 0.00 0.00 2.57
113 114 1.434555 CGGCGGTGTACAATCAAAGA 58.565 50.000 0.00 0.00 0.00 2.52
195 196 7.404139 ACGTTCACTTGTCTATTCTTTGTAC 57.596 36.000 0.00 0.00 0.00 2.90
213 214 6.777213 TTGTACTGGCCTTTGTTTTTCTTA 57.223 33.333 3.32 0.00 0.00 2.10
246 247 6.429385 CCAGATCTAAGATATCTTTTGGGTGC 59.571 42.308 22.60 7.13 37.40 5.01
247 248 7.222872 CAGATCTAAGATATCTTTTGGGTGCT 58.777 38.462 22.60 9.02 37.40 4.40
305 307 4.200874 TGTTCTTCATACCGGTTGTTTGT 58.799 39.130 15.04 0.00 0.00 2.83
337 339 5.819379 TGATGAAAGTGATAGAAGCACCATC 59.181 40.000 0.00 0.00 36.95 3.51
364 366 2.286184 GCGGGATAAACTAACACATGCG 60.286 50.000 0.00 0.00 0.00 4.73
369 371 4.024048 GGATAAACTAACACATGCGGATGG 60.024 45.833 21.55 12.21 33.39 3.51
385 387 4.559300 GCGGATGGGATATTTTGGTTCATG 60.559 45.833 0.00 0.00 0.00 3.07
402 529 6.772233 TGGTTCATGTTGGATAATATGTCTGG 59.228 38.462 0.00 0.00 36.91 3.86
580 1263 9.502091 TTGACAGTTTTAAGCATCATTAGTACT 57.498 29.630 0.00 0.00 0.00 2.73
581 1264 9.151471 TGACAGTTTTAAGCATCATTAGTACTC 57.849 33.333 0.00 0.00 0.00 2.59
582 1265 8.494016 ACAGTTTTAAGCATCATTAGTACTCC 57.506 34.615 0.00 0.00 0.00 3.85
713 1396 3.980775 CACCACGAAATTTTCTTGCGAAT 59.019 39.130 9.49 0.00 0.00 3.34
795 1479 3.051479 GTTACCGGGCCGTGGTTG 61.051 66.667 26.32 11.62 40.96 3.77
833 1517 2.510411 CCAGCCCATGTATCCGCA 59.490 61.111 0.00 0.00 0.00 5.69
896 1582 2.633509 GCAAGTGAAGCCTGCCAGG 61.634 63.158 6.32 6.32 38.80 4.45
985 1672 2.855514 TTTCCAGTTGCAAGCCGCC 61.856 57.895 0.00 0.00 41.33 6.13
1102 1792 2.965831 TCCCTACTCTTGATCGATTGGG 59.034 50.000 0.00 0.00 0.00 4.12
1178 1868 0.530650 CTGTAGATCCGTGGCGCAAT 60.531 55.000 10.83 0.00 0.00 3.56
1231 1924 3.242511 CGTGTTCGATGTGCATGATTCAT 60.243 43.478 0.00 0.00 39.71 2.57
1260 1954 7.160726 CCTTGGATTGTTTGATGGTTTTATGT 58.839 34.615 0.00 0.00 0.00 2.29
1382 2076 1.503542 CAGCAACGCCAAGGACATC 59.496 57.895 0.00 0.00 0.00 3.06
1475 2173 7.148289 GCTGCCGAGTAATACTAGTATATGTCA 60.148 40.741 15.74 7.18 0.00 3.58
1534 2236 1.501582 AGGCCTCTCTTGGTATGGTC 58.498 55.000 0.00 0.00 0.00 4.02
1537 2239 2.420687 GGCCTCTCTTGGTATGGTCAAG 60.421 54.545 0.00 0.00 41.99 3.02
1546 2248 5.705441 TCTTGGTATGGTCAAGCAGTTTTAG 59.295 40.000 0.00 0.00 40.82 1.85
1547 2249 3.756434 TGGTATGGTCAAGCAGTTTTAGC 59.244 43.478 0.00 0.00 0.00 3.09
1548 2250 3.128764 GGTATGGTCAAGCAGTTTTAGCC 59.871 47.826 0.00 0.00 0.00 3.93
1550 2252 2.504367 TGGTCAAGCAGTTTTAGCCTC 58.496 47.619 0.00 0.00 0.00 4.70
1552 2254 2.744741 GGTCAAGCAGTTTTAGCCTCTC 59.255 50.000 0.00 0.00 0.00 3.20
1553 2255 3.558109 GGTCAAGCAGTTTTAGCCTCTCT 60.558 47.826 0.00 0.00 0.00 3.10
1554 2256 4.068599 GTCAAGCAGTTTTAGCCTCTCTT 58.931 43.478 0.00 0.00 0.00 2.85
1555 2257 4.067896 TCAAGCAGTTTTAGCCTCTCTTG 58.932 43.478 0.00 0.00 0.00 3.02
1587 2305 5.483811 TGGTACATACTGTGGTGTAATGTG 58.516 41.667 8.73 0.00 33.05 3.21
1682 2514 5.471556 TTTGCAATCATCACCTCATGTTT 57.528 34.783 0.00 0.00 0.00 2.83
1714 2548 7.595875 TGCAATGTTTTGTATCTGTTTGATCAG 59.404 33.333 0.00 0.00 35.17 2.90
1728 2562 7.175467 TCTGTTTGATCAGTGTGCAATTTCTAT 59.825 33.333 0.00 0.00 36.85 1.98
1729 2563 7.660112 TGTTTGATCAGTGTGCAATTTCTATT 58.340 30.769 0.00 0.00 0.00 1.73
1730 2564 8.791675 TGTTTGATCAGTGTGCAATTTCTATTA 58.208 29.630 0.00 0.00 0.00 0.98
1751 2585 4.322057 AACCATAAGGCATCTTGGAACT 57.678 40.909 6.55 0.00 39.06 3.01
1856 2696 6.376299 CCCCAGTTTCAACTATTTACTAACCC 59.624 42.308 0.00 0.00 37.08 4.11
2025 2904 6.923928 ATGTTGTTTCCATTTCCACTTTTG 57.076 33.333 0.00 0.00 0.00 2.44
2041 2922 6.934645 TCCACTTTTGTCTGATTAACTGTAGG 59.065 38.462 0.00 0.00 0.00 3.18
2045 2926 9.185680 ACTTTTGTCTGATTAACTGTAGGTTTT 57.814 29.630 0.00 0.00 39.17 2.43
2060 2941 9.260002 ACTGTAGGTTTTATGCTTCAATTTTTG 57.740 29.630 0.00 0.00 0.00 2.44
2125 3006 5.119931 TGAATACCTGAATGTTTGTGTGC 57.880 39.130 0.00 0.00 0.00 4.57
2136 3022 4.217754 TGTTTGTGTGCGACTAATTTCC 57.782 40.909 0.00 0.00 0.00 3.13
2198 3092 5.655974 ACTGATCTCTGAATCTGCACTCTTA 59.344 40.000 0.00 0.00 0.00 2.10
2242 3136 2.001076 AACCTCAAAGGAAGCAAGGG 57.999 50.000 0.00 0.00 37.67 3.95
2277 3172 1.202639 ACGAACTGTGGTGCTTCATCA 60.203 47.619 0.00 0.00 0.00 3.07
2280 3175 2.645838 ACTGTGGTGCTTCATCAAGT 57.354 45.000 0.00 0.00 31.45 3.16
2399 3294 5.739161 GCATGTGAAACCGATAATTCTGTTC 59.261 40.000 0.00 0.00 34.36 3.18
2555 3464 3.882888 AGTCTCTGCTGTGCTCTACTATC 59.117 47.826 0.00 0.00 0.00 2.08
2557 3466 2.295909 CTCTGCTGTGCTCTACTATCCC 59.704 54.545 0.00 0.00 0.00 3.85
2565 3476 2.243810 GCTCTACTATCCCCTCTGTGG 58.756 57.143 0.00 0.00 0.00 4.17
2633 3547 7.025963 CCTGACTTTGCTTAAGCTAGAAAATG 58.974 38.462 26.90 16.18 42.66 2.32
2688 3602 3.413846 TGTCAATGCTGAGCTTCTCTT 57.586 42.857 5.83 0.00 30.14 2.85
2690 3604 3.244318 TGTCAATGCTGAGCTTCTCTTGA 60.244 43.478 5.83 4.65 30.14 3.02
2742 3656 4.695455 AGTGGAATTATTCGTTGGTCACAG 59.305 41.667 10.62 0.00 0.00 3.66
2744 3658 5.180492 GTGGAATTATTCGTTGGTCACAGAA 59.820 40.000 0.00 0.00 0.00 3.02
2746 3660 6.263392 TGGAATTATTCGTTGGTCACAGAAAA 59.737 34.615 0.00 0.00 0.00 2.29
2748 3662 7.114388 GGAATTATTCGTTGGTCACAGAAAAAC 59.886 37.037 0.00 0.00 0.00 2.43
2749 3663 3.768468 TTCGTTGGTCACAGAAAAACC 57.232 42.857 0.00 0.00 0.00 3.27
2750 3664 1.666700 TCGTTGGTCACAGAAAAACCG 59.333 47.619 0.00 0.00 35.76 4.44
2751 3665 1.835121 GTTGGTCACAGAAAAACCGC 58.165 50.000 0.00 0.00 35.76 5.68
2754 3668 1.104577 GGTCACAGAAAAACCGCCCA 61.105 55.000 0.00 0.00 0.00 5.36
2756 3670 1.135333 GTCACAGAAAAACCGCCCAAA 59.865 47.619 0.00 0.00 0.00 3.28
2757 3671 2.035632 TCACAGAAAAACCGCCCAAAT 58.964 42.857 0.00 0.00 0.00 2.32
2758 3672 2.432510 TCACAGAAAAACCGCCCAAATT 59.567 40.909 0.00 0.00 0.00 1.82
2759 3673 2.543430 CACAGAAAAACCGCCCAAATTG 59.457 45.455 0.00 0.00 0.00 2.32
2760 3674 2.169561 ACAGAAAAACCGCCCAAATTGT 59.830 40.909 0.00 0.00 0.00 2.71
2761 3675 3.202097 CAGAAAAACCGCCCAAATTGTT 58.798 40.909 0.00 0.00 0.00 2.83
2763 3677 4.811557 CAGAAAAACCGCCCAAATTGTTAA 59.188 37.500 0.00 0.00 0.00 2.01
2764 3678 5.294552 CAGAAAAACCGCCCAAATTGTTAAA 59.705 36.000 0.00 0.00 0.00 1.52
2765 3679 6.017523 CAGAAAAACCGCCCAAATTGTTAAAT 60.018 34.615 0.00 0.00 0.00 1.40
2766 3680 5.681337 AAAACCGCCCAAATTGTTAAATG 57.319 34.783 0.00 0.00 0.00 2.32
2767 3681 3.326836 ACCGCCCAAATTGTTAAATGG 57.673 42.857 0.00 0.00 0.00 3.16
2768 3682 2.635427 ACCGCCCAAATTGTTAAATGGT 59.365 40.909 0.00 0.00 0.00 3.55
2769 3683 3.258228 CCGCCCAAATTGTTAAATGGTC 58.742 45.455 0.00 0.00 0.00 4.02
2770 3684 3.306364 CCGCCCAAATTGTTAAATGGTCA 60.306 43.478 0.00 0.00 0.00 4.02
2771 3685 4.502962 CGCCCAAATTGTTAAATGGTCAT 58.497 39.130 0.00 0.00 0.00 3.06
2772 3686 4.566360 CGCCCAAATTGTTAAATGGTCATC 59.434 41.667 0.00 0.00 0.00 2.92
2820 3737 1.686355 CTACCGCCCATATTTTGCCA 58.314 50.000 0.00 0.00 0.00 4.92
2883 3801 3.056107 CCACCCTCTTGTTCTAATCGTGA 60.056 47.826 0.00 0.00 0.00 4.35
2926 3846 0.654683 GATCTGACAGCCAACGATGC 59.345 55.000 0.00 0.00 0.00 3.91
2932 3852 0.244450 ACAGCCAACGATGCCAAATG 59.756 50.000 0.00 0.00 0.00 2.32
2933 3853 0.527113 CAGCCAACGATGCCAAATGA 59.473 50.000 0.00 0.00 0.00 2.57
2934 3854 1.135527 CAGCCAACGATGCCAAATGAT 59.864 47.619 0.00 0.00 0.00 2.45
2951 3871 6.466326 CCAAATGATACCTGTATCCCACTCAT 60.466 42.308 13.30 0.22 40.84 2.90
2953 3873 7.872061 AATGATACCTGTATCCCACTCATAA 57.128 36.000 13.30 0.00 40.84 1.90
2957 3877 8.156820 TGATACCTGTATCCCACTCATAATTTG 58.843 37.037 13.30 0.00 40.84 2.32
2981 3901 6.052840 AGCATGTATCACATCGTCAAAATC 57.947 37.500 0.00 0.00 36.53 2.17
2985 3905 3.933155 ATCACATCGTCAAAATCGAGC 57.067 42.857 0.00 0.00 40.57 5.03
2996 3916 1.961180 AAATCGAGCGTCTCCAGGGG 61.961 60.000 0.00 0.00 0.00 4.79
3013 3933 0.881796 GGGTTAGGTGTGCTTTCTGC 59.118 55.000 0.00 0.00 43.25 4.26
3018 3938 0.536006 AGGTGTGCTTTCTGCTGTCC 60.536 55.000 0.00 0.00 43.37 4.02
3040 3960 4.800993 CCTTTTGTATTTGTGCGTGAACAA 59.199 37.500 0.00 0.00 38.26 2.83
3041 3961 5.051774 CCTTTTGTATTTGTGCGTGAACAAG 60.052 40.000 0.00 0.00 40.93 3.16
3045 3965 1.837648 TTTGTGCGTGAACAAGCATG 58.162 45.000 16.80 0.00 46.50 4.06
3050 3970 0.110056 GCGTGAACAAGCATGAGTGG 60.110 55.000 0.00 0.00 35.86 4.00
3058 3978 6.749118 GTGAACAAGCATGAGTGGAATTATTC 59.251 38.462 0.00 0.00 0.00 1.75
3071 3991 4.127907 GGAATTATTCCTTCGTCACCTCC 58.872 47.826 16.16 0.00 46.57 4.30
3072 3992 4.141688 GGAATTATTCCTTCGTCACCTCCT 60.142 45.833 16.16 0.00 46.57 3.69
3073 3993 3.887621 TTATTCCTTCGTCACCTCCTG 57.112 47.619 0.00 0.00 0.00 3.86
3074 3994 1.938585 ATTCCTTCGTCACCTCCTGA 58.061 50.000 0.00 0.00 0.00 3.86
3075 3995 1.712056 TTCCTTCGTCACCTCCTGAA 58.288 50.000 0.00 0.00 0.00 3.02
3076 3996 1.938585 TCCTTCGTCACCTCCTGAAT 58.061 50.000 0.00 0.00 0.00 2.57
3077 3997 3.095912 TCCTTCGTCACCTCCTGAATA 57.904 47.619 0.00 0.00 0.00 1.75
3078 3998 3.437213 TCCTTCGTCACCTCCTGAATAA 58.563 45.455 0.00 0.00 0.00 1.40
3079 3999 3.835978 TCCTTCGTCACCTCCTGAATAAA 59.164 43.478 0.00 0.00 0.00 1.40
3080 4000 4.081642 TCCTTCGTCACCTCCTGAATAAAG 60.082 45.833 0.00 0.00 0.00 1.85
3081 4001 4.322801 CCTTCGTCACCTCCTGAATAAAGT 60.323 45.833 0.00 0.00 0.00 2.66
3082 4002 5.105473 CCTTCGTCACCTCCTGAATAAAGTA 60.105 44.000 0.00 0.00 0.00 2.24
3083 4003 5.578005 TCGTCACCTCCTGAATAAAGTAG 57.422 43.478 0.00 0.00 0.00 2.57
3084 4004 5.258841 TCGTCACCTCCTGAATAAAGTAGA 58.741 41.667 0.00 0.00 0.00 2.59
3085 4005 5.713389 TCGTCACCTCCTGAATAAAGTAGAA 59.287 40.000 0.00 0.00 0.00 2.10
3086 4006 6.380274 TCGTCACCTCCTGAATAAAGTAGAAT 59.620 38.462 0.00 0.00 0.00 2.40
3087 4007 7.042335 CGTCACCTCCTGAATAAAGTAGAATT 58.958 38.462 0.00 0.00 0.00 2.17
3088 4008 7.222999 CGTCACCTCCTGAATAAAGTAGAATTC 59.777 40.741 0.00 0.00 33.57 2.17
3089 4009 8.261522 GTCACCTCCTGAATAAAGTAGAATTCT 58.738 37.037 13.56 13.56 34.00 2.40
3090 4010 8.826765 TCACCTCCTGAATAAAGTAGAATTCTT 58.173 33.333 14.36 0.00 34.00 2.52
3127 4047 7.695480 AAAAGAGAATAGAAAGCTTTCCCTC 57.305 36.000 30.83 27.43 37.92 4.30
3128 4048 6.380079 AAGAGAATAGAAAGCTTTCCCTCA 57.620 37.500 30.83 16.73 37.92 3.86
3129 4049 6.380079 AGAGAATAGAAAGCTTTCCCTCAA 57.620 37.500 30.83 14.81 37.92 3.02
3130 4050 6.784031 AGAGAATAGAAAGCTTTCCCTCAAA 58.216 36.000 30.83 13.25 37.92 2.69
3131 4051 7.234355 AGAGAATAGAAAGCTTTCCCTCAAAA 58.766 34.615 30.83 11.71 37.92 2.44
3132 4052 7.725844 AGAGAATAGAAAGCTTTCCCTCAAAAA 59.274 33.333 30.83 10.50 37.92 1.94
3155 4075 6.885952 AAAAAGAGAGTAGAAAGCTTTCCC 57.114 37.500 30.83 22.60 37.92 3.97
3156 4076 5.834281 AAAGAGAGTAGAAAGCTTTCCCT 57.166 39.130 30.83 26.24 37.92 4.20
3157 4077 5.414789 AAGAGAGTAGAAAGCTTTCCCTC 57.585 43.478 30.77 30.77 37.92 4.30
3158 4078 4.421131 AGAGAGTAGAAAGCTTTCCCTCA 58.579 43.478 34.79 20.27 37.77 3.86
3159 4079 4.841246 AGAGAGTAGAAAGCTTTCCCTCAA 59.159 41.667 34.79 18.70 37.77 3.02
3160 4080 5.308237 AGAGAGTAGAAAGCTTTCCCTCAAA 59.692 40.000 34.79 17.42 37.77 2.69
3161 4081 5.941788 AGAGTAGAAAGCTTTCCCTCAAAA 58.058 37.500 34.79 16.17 37.77 2.44
3162 4082 6.365520 AGAGTAGAAAGCTTTCCCTCAAAAA 58.634 36.000 34.79 15.17 37.77 1.94
3187 4107 7.722795 AAAAGAGAGTAGAAAGCTTTCACTC 57.277 36.000 34.96 34.96 40.95 3.51
3188 4108 6.412362 AAGAGAGTAGAAAGCTTTCACTCA 57.588 37.500 38.17 24.15 41.88 3.41
3189 4109 6.412362 AGAGAGTAGAAAGCTTTCACTCAA 57.588 37.500 38.17 22.70 41.88 3.02
3190 4110 6.821388 AGAGAGTAGAAAGCTTTCACTCAAA 58.179 36.000 38.17 21.53 41.88 2.69
3191 4111 7.275920 AGAGAGTAGAAAGCTTTCACTCAAAA 58.724 34.615 38.17 20.38 41.88 2.44
3192 4112 7.770897 AGAGAGTAGAAAGCTTTCACTCAAAAA 59.229 33.333 38.17 19.46 41.88 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.083489 TTTGAAGACCGCAATAGCCG 58.917 50.000 0.00 0.00 37.52 5.52
21 22 1.344953 AATGCCCTCGCCATACCAGA 61.345 55.000 0.00 0.00 0.00 3.86
45 46 4.201676 CCAACAGCAAAGAAAAACGAAACC 60.202 41.667 0.00 0.00 0.00 3.27
62 63 9.003658 AGATTAAGAATTACACTGAACCAACAG 57.996 33.333 0.00 0.00 42.78 3.16
99 100 9.788960 AGTCTTTTTCTTTCTTTGATTGTACAC 57.211 29.630 0.00 0.00 0.00 2.90
169 170 7.639162 ACAAAGAATAGACAAGTGAACGTAG 57.361 36.000 0.00 0.00 0.00 3.51
172 173 7.359264 CCAGTACAAAGAATAGACAAGTGAACG 60.359 40.741 0.00 0.00 0.00 3.95
234 235 8.620416 GTTTTTGAATAAAAGCACCCAAAAGAT 58.380 29.630 0.00 0.00 37.08 2.40
235 236 7.607991 TGTTTTTGAATAAAAGCACCCAAAAGA 59.392 29.630 0.00 0.00 40.54 2.52
305 307 6.207691 TCTATCACTTTCATCATCGTGACA 57.792 37.500 0.00 0.00 38.99 3.58
337 339 0.179067 TTAGTTTATCCCGCCGCCTG 60.179 55.000 0.00 0.00 0.00 4.85
345 347 3.537580 TCCGCATGTGTTAGTTTATCCC 58.462 45.455 5.38 0.00 0.00 3.85
364 366 6.282930 CAACATGAACCAAAATATCCCATCC 58.717 40.000 0.00 0.00 0.00 3.51
385 387 7.730364 ATCGTTTCCAGACATATTATCCAAC 57.270 36.000 0.00 0.00 0.00 3.77
467 594 3.257469 AGCCGATACGACCGATATAGA 57.743 47.619 0.00 0.00 0.00 1.98
475 604 6.833342 TTTTAAATCTAAGCCGATACGACC 57.167 37.500 0.00 0.00 0.00 4.79
481 610 5.878669 ACCGAGTTTTTAAATCTAAGCCGAT 59.121 36.000 0.00 0.00 0.00 4.18
483 612 5.106830 ACACCGAGTTTTTAAATCTAAGCCG 60.107 40.000 0.00 0.00 0.00 5.52
579 1262 8.488651 AAAAGATACTACCAACAAATACGGAG 57.511 34.615 0.00 0.00 0.00 4.63
580 1263 8.095792 TGAAAAGATACTACCAACAAATACGGA 58.904 33.333 0.00 0.00 0.00 4.69
581 1264 8.259049 TGAAAAGATACTACCAACAAATACGG 57.741 34.615 0.00 0.00 0.00 4.02
582 1265 8.932791 ACTGAAAAGATACTACCAACAAATACG 58.067 33.333 0.00 0.00 0.00 3.06
619 1302 0.608640 AACGCTGTCTTCGGGAATCT 59.391 50.000 0.00 0.00 0.00 2.40
713 1396 8.895737 ACTCCAAATTTCGTAGTGTTCTTTTTA 58.104 29.630 0.00 0.00 0.00 1.52
778 1462 3.051479 CAACCACGGCCCGGTAAC 61.051 66.667 8.57 0.00 34.99 2.50
795 1479 1.940613 CCTCACAGCCCGTATTTAAGC 59.059 52.381 0.00 0.00 0.00 3.09
896 1582 1.730612 GCGCCGGGTTTTCTATATAGC 59.269 52.381 2.18 0.00 0.00 2.97
1102 1792 1.078637 GAGGGCGGGGTACAAGTTC 60.079 63.158 0.00 0.00 0.00 3.01
1178 1868 6.945938 AAGATTTAGAGCTAAGCTACGAGA 57.054 37.500 0.00 0.00 39.88 4.04
1231 1924 1.067706 CATCAAACAATCCAAGGCGCA 60.068 47.619 10.83 0.00 0.00 6.09
1382 2076 0.583438 CGCATACCTTGATGAAGCCG 59.417 55.000 0.00 0.00 0.00 5.52
1506 2208 2.093764 CCAAGAGAGGCCTTGTAGACAG 60.094 54.545 6.77 0.00 41.34 3.51
1534 2236 3.190118 CCAAGAGAGGCTAAAACTGCTTG 59.810 47.826 0.00 0.00 33.26 4.01
1547 2249 2.242043 ACCAACAAATGCCAAGAGAGG 58.758 47.619 0.00 0.00 0.00 3.69
1548 2250 3.820467 TGTACCAACAAATGCCAAGAGAG 59.180 43.478 0.00 0.00 30.91 3.20
1550 2252 4.789012 ATGTACCAACAAATGCCAAGAG 57.211 40.909 0.00 0.00 39.58 2.85
1552 2254 5.401550 CAGTATGTACCAACAAATGCCAAG 58.598 41.667 0.00 0.00 39.58 3.61
1553 2255 5.384063 CAGTATGTACCAACAAATGCCAA 57.616 39.130 0.00 0.00 39.58 4.52
1612 2330 4.655963 AGGAGCAACACACACATCTATTT 58.344 39.130 0.00 0.00 0.00 1.40
1714 2548 7.435192 GCCTTATGGTTAATAGAAATTGCACAC 59.565 37.037 0.00 0.00 35.27 3.82
1728 2562 5.652014 CAGTTCCAAGATGCCTTATGGTTAA 59.348 40.000 0.00 0.00 35.27 2.01
1729 2563 5.045213 TCAGTTCCAAGATGCCTTATGGTTA 60.045 40.000 0.00 0.00 35.27 2.85
1730 2564 4.019174 CAGTTCCAAGATGCCTTATGGTT 58.981 43.478 0.00 0.00 35.27 3.67
1751 2585 2.916702 AGTCATGCACAACTCTGTCA 57.083 45.000 0.00 0.00 31.64 3.58
1782 2620 1.896660 TGGGAGCAACAAACGGAGC 60.897 57.895 0.00 0.00 0.00 4.70
1783 2621 1.515521 GGTGGGAGCAACAAACGGAG 61.516 60.000 0.00 0.00 0.00 4.63
1885 2726 2.170187 TGTTATGCATTGAAATGGGCCC 59.830 45.455 17.59 17.59 36.90 5.80
2025 2904 8.494016 AGCATAAAACCTACAGTTAATCAGAC 57.506 34.615 0.00 0.00 37.88 3.51
2041 2922 7.647318 CCAAACCCAAAAATTGAAGCATAAAAC 59.353 33.333 0.00 0.00 0.00 2.43
2045 2926 5.163152 ACCCAAACCCAAAAATTGAAGCATA 60.163 36.000 0.00 0.00 0.00 3.14
2060 2941 9.733556 AATCTGAAAAATAATTTACCCAAACCC 57.266 29.630 0.00 0.00 0.00 4.11
2095 2976 4.603131 ACATTCAGGTATTCAGGCACAAT 58.397 39.130 0.00 0.00 0.00 2.71
2125 3006 6.436843 AAAAGGCATACAGGAAATTAGTCG 57.563 37.500 0.00 0.00 0.00 4.18
2188 3082 5.867716 ACGGTACTGTTAAATAAGAGTGCAG 59.132 40.000 16.35 14.93 41.60 4.41
2198 3092 8.851541 TTCCATTCTTAACGGTACTGTTAAAT 57.148 30.769 30.36 22.45 42.10 1.40
2242 3136 6.456988 CCACAGTTCGTTGATAATTTCCTAGC 60.457 42.308 0.00 0.00 0.00 3.42
2321 3216 5.453198 GGTTTTGTCACCAGGATTCAAACAT 60.453 40.000 0.00 0.00 36.73 2.71
2346 3241 4.456911 CAGCAGTCACTAACATGGTTTCAT 59.543 41.667 0.00 0.00 0.00 2.57
2399 3294 1.750193 AACCATAATGGCACGACAGG 58.250 50.000 0.00 0.00 42.67 4.00
2457 3352 3.884704 AAAGCATGGCCGGCCTTCA 62.885 57.895 43.34 26.79 36.94 3.02
2514 3412 5.869579 AGACTGATTAAGAACAGAAGCCAA 58.130 37.500 12.02 0.00 37.54 4.52
2555 3464 3.433306 TCATAAACAACCACAGAGGGG 57.567 47.619 0.00 0.00 43.89 4.79
2557 3466 6.207417 ACAAAGATCATAAACAACCACAGAGG 59.793 38.462 0.00 0.00 45.67 3.69
2565 3476 9.900264 GTTCAACAAACAAAGATCATAAACAAC 57.100 29.630 0.00 0.00 37.82 3.32
2633 3547 8.730680 AGATGACCATTTAACAATTACAGACAC 58.269 33.333 0.00 0.00 0.00 3.67
2688 3602 1.855295 TGACCCGCACCTAATACTCA 58.145 50.000 0.00 0.00 0.00 3.41
2690 3604 3.244630 TGTTTTGACCCGCACCTAATACT 60.245 43.478 0.00 0.00 0.00 2.12
2742 3656 5.736486 TTTAACAATTTGGGCGGTTTTTC 57.264 34.783 0.78 0.00 0.00 2.29
2744 3658 4.517075 CCATTTAACAATTTGGGCGGTTTT 59.483 37.500 0.78 0.00 0.00 2.43
2746 3660 3.071747 ACCATTTAACAATTTGGGCGGTT 59.928 39.130 0.78 0.00 33.39 4.44
2748 3662 3.258228 GACCATTTAACAATTTGGGCGG 58.742 45.455 0.78 0.00 33.39 6.13
2749 3663 3.919216 TGACCATTTAACAATTTGGGCG 58.081 40.909 0.78 0.00 40.35 6.13
2750 3664 5.733676 AGATGACCATTTAACAATTTGGGC 58.266 37.500 0.78 0.00 37.80 5.36
2763 3677 7.010830 CGCATCGAATTCATATAGATGACCATT 59.989 37.037 18.74 0.00 41.92 3.16
2764 3678 6.478016 CGCATCGAATTCATATAGATGACCAT 59.522 38.462 18.74 0.00 41.92 3.55
2765 3679 5.807011 CGCATCGAATTCATATAGATGACCA 59.193 40.000 18.74 0.00 41.92 4.02
2766 3680 5.276584 GCGCATCGAATTCATATAGATGACC 60.277 44.000 18.74 8.59 41.92 4.02
2767 3681 5.553396 CGCGCATCGAATTCATATAGATGAC 60.553 44.000 18.74 11.34 40.26 3.06
2768 3682 4.500477 CGCGCATCGAATTCATATAGATGA 59.500 41.667 18.74 0.00 40.62 2.92
2769 3683 4.500477 TCGCGCATCGAATTCATATAGATG 59.500 41.667 8.75 13.07 45.36 2.90
2770 3684 4.672409 TCGCGCATCGAATTCATATAGAT 58.328 39.130 8.75 0.00 45.36 1.98
2771 3685 4.091453 TCGCGCATCGAATTCATATAGA 57.909 40.909 8.75 0.00 45.36 1.98
2783 3697 3.250323 CAGGACAGTCGCGCATCG 61.250 66.667 8.75 0.00 40.15 3.84
2836 3753 0.035439 AATTGTTGGCCTCCGACGAT 60.035 50.000 3.32 0.14 42.30 3.73
2926 3846 5.163205 TGAGTGGGATACAGGTATCATTTGG 60.163 44.000 18.30 0.00 42.76 3.28
2932 3852 8.375506 TCAAATTATGAGTGGGATACAGGTATC 58.624 37.037 10.31 10.31 36.48 2.24
2933 3853 8.275187 TCAAATTATGAGTGGGATACAGGTAT 57.725 34.615 0.00 0.00 33.16 2.73
2934 3854 7.684317 TCAAATTATGAGTGGGATACAGGTA 57.316 36.000 0.00 0.00 33.16 3.08
2951 3871 6.760770 TGACGATGTGATACATGCTCAAATTA 59.239 34.615 0.00 0.00 39.27 1.40
2953 3873 5.118286 TGACGATGTGATACATGCTCAAAT 58.882 37.500 0.00 2.02 39.27 2.32
2957 3877 5.469373 TTTTGACGATGTGATACATGCTC 57.531 39.130 0.00 0.00 39.27 4.26
2964 3884 3.485743 CGCTCGATTTTGACGATGTGATA 59.514 43.478 0.00 0.00 39.02 2.15
2972 3892 0.640768 GGAGACGCTCGATTTTGACG 59.359 55.000 0.00 0.00 0.00 4.35
2981 3901 2.005960 CTAACCCCTGGAGACGCTCG 62.006 65.000 0.00 0.00 0.00 5.03
2985 3905 0.903454 ACACCTAACCCCTGGAGACG 60.903 60.000 0.00 0.00 0.00 4.18
3013 3933 3.974401 CACGCACAAATACAAAAGGACAG 59.026 43.478 0.00 0.00 0.00 3.51
3018 3938 5.554324 GCTTGTTCACGCACAAATACAAAAG 60.554 40.000 0.00 0.00 36.22 2.27
3050 3970 4.811557 CAGGAGGTGACGAAGGAATAATTC 59.188 45.833 0.00 0.00 0.00 2.17
3058 3978 3.887621 TTATTCAGGAGGTGACGAAGG 57.112 47.619 0.00 0.00 33.71 3.46
3059 3979 4.822026 ACTTTATTCAGGAGGTGACGAAG 58.178 43.478 0.00 0.00 33.71 3.79
3060 3980 4.884668 ACTTTATTCAGGAGGTGACGAA 57.115 40.909 0.00 0.00 33.71 3.85
3061 3981 5.258841 TCTACTTTATTCAGGAGGTGACGA 58.741 41.667 0.00 0.00 33.71 4.20
3062 3982 5.578005 TCTACTTTATTCAGGAGGTGACG 57.422 43.478 0.00 0.00 33.71 4.35
3063 3983 8.261522 AGAATTCTACTTTATTCAGGAGGTGAC 58.738 37.037 6.06 0.00 33.71 3.67
3064 3984 8.380742 AGAATTCTACTTTATTCAGGAGGTGA 57.619 34.615 6.06 0.00 34.06 4.02
3102 4022 7.725844 TGAGGGAAAGCTTTCTATTCTCTTTTT 59.274 33.333 32.28 9.48 34.12 1.94
3103 4023 7.234355 TGAGGGAAAGCTTTCTATTCTCTTTT 58.766 34.615 32.28 10.68 34.12 2.27
3104 4024 6.784031 TGAGGGAAAGCTTTCTATTCTCTTT 58.216 36.000 32.28 11.81 34.12 2.52
3105 4025 6.380079 TGAGGGAAAGCTTTCTATTCTCTT 57.620 37.500 32.28 15.28 34.12 2.85
3106 4026 6.380079 TTGAGGGAAAGCTTTCTATTCTCT 57.620 37.500 32.28 17.00 36.62 3.10
3107 4027 7.454260 TTTTGAGGGAAAGCTTTCTATTCTC 57.546 36.000 32.28 28.62 37.35 2.87
3108 4028 7.839680 TTTTTGAGGGAAAGCTTTCTATTCT 57.160 32.000 32.28 24.11 37.35 2.40
3132 4052 6.606069 AGGGAAAGCTTTCTACTCTCTTTTT 58.394 36.000 32.28 9.86 37.35 1.94
3133 4053 6.183361 TGAGGGAAAGCTTTCTACTCTCTTTT 60.183 38.462 35.92 19.01 39.52 2.27
3134 4054 5.308237 TGAGGGAAAGCTTTCTACTCTCTTT 59.692 40.000 35.92 19.47 39.52 2.52
3135 4055 4.841246 TGAGGGAAAGCTTTCTACTCTCTT 59.159 41.667 35.92 21.62 39.52 2.85
3136 4056 4.421131 TGAGGGAAAGCTTTCTACTCTCT 58.579 43.478 35.92 23.36 39.52 3.10
3137 4057 4.810191 TGAGGGAAAGCTTTCTACTCTC 57.190 45.455 35.92 31.16 39.52 3.20
3138 4058 5.568620 TTTGAGGGAAAGCTTTCTACTCT 57.431 39.130 35.92 27.84 39.52 3.24
3139 4059 6.635030 TTTTTGAGGGAAAGCTTTCTACTC 57.365 37.500 33.41 33.41 39.39 2.59
3162 4082 7.770897 TGAGTGAAAGCTTTCTACTCTCTTTTT 59.229 33.333 37.33 21.54 41.08 1.94
3163 4083 7.275920 TGAGTGAAAGCTTTCTACTCTCTTTT 58.724 34.615 37.33 21.98 41.08 2.27
3164 4084 6.821388 TGAGTGAAAGCTTTCTACTCTCTTT 58.179 36.000 37.33 22.41 41.08 2.52
3165 4085 6.412362 TGAGTGAAAGCTTTCTACTCTCTT 57.588 37.500 37.33 22.84 41.08 2.85
3166 4086 6.412362 TTGAGTGAAAGCTTTCTACTCTCT 57.588 37.500 37.33 26.69 41.08 3.10
3167 4087 7.484035 TTTTGAGTGAAAGCTTTCTACTCTC 57.516 36.000 37.33 32.33 41.08 3.20
3168 4088 7.865706 TTTTTGAGTGAAAGCTTTCTACTCT 57.134 32.000 37.33 29.27 41.08 3.24


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

AutoCloner maintained by Alex Coulton.