Multiple sequence alignment - TraesCS1D01G452100

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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 TraesCS1D01G452100 chr1D 100.000 2518 0 0 1 2518 493783541 493781024 0.000000e+00 4650.0
1 TraesCS1D01G452100 chr1D 83.175 737 78 27 931 1651 494306796 494307502 1.270000e-177 632.0
2 TraesCS1D01G452100 chr1D 86.477 562 60 9 930 1491 494349692 494350237 9.960000e-169 603.0
3 TraesCS1D01G452100 chr1D 96.491 114 4 0 2405 2518 493776317 493776204 3.310000e-44 189.0
4 TraesCS1D01G452100 chr1D 91.026 78 5 2 1577 1654 494169716 494169791 1.230000e-18 104.0
5 TraesCS1D01G452100 chr1A 90.394 1728 72 33 708 2400 592100472 592098804 0.000000e+00 2185.0
6 TraesCS1D01G452100 chr1A 89.601 702 39 13 18 717 592101243 592100574 0.000000e+00 861.0
7 TraesCS1D01G452100 chr1A 87.722 562 56 6 930 1491 592994265 592994813 0.000000e+00 643.0
8 TraesCS1D01G452100 chr1A 93.043 115 8 0 2404 2518 465191450 465191564 4.310000e-38 169.0
9 TraesCS1D01G452100 chr1A 92.308 117 9 0 2402 2518 465196268 465196384 1.550000e-37 167.0
10 TraesCS1D01G452100 chr1A 85.714 154 16 3 753 906 592994122 592994269 9.320000e-35 158.0
11 TraesCS1D01G452100 chr1B 85.843 1222 73 42 787 1992 686854015 686852878 0.000000e+00 1206.0
12 TraesCS1D01G452100 chr1B 85.464 743 47 29 1 717 686855051 686854344 0.000000e+00 717.0
13 TraesCS1D01G452100 chr1B 86.833 562 60 6 930 1491 687531409 687531956 1.280000e-172 616.0
14 TraesCS1D01G452100 chr1B 90.732 205 7 4 2147 2341 686852723 686852521 1.920000e-66 263.0
15 TraesCS1D01G452100 chr1B 94.805 77 2 1 2069 2143 686852851 686852775 4.400000e-23 119.0
16 TraesCS1D01G452100 chr1B 88.235 85 2 4 708 791 686854254 686854177 7.420000e-16 95.3
17 TraesCS1D01G452100 chrUn 86.501 563 60 7 931 1491 290638879 290638331 2.770000e-169 604.0
18 TraesCS1D01G452100 chrUn 86.501 563 60 7 931 1491 290644604 290644056 2.770000e-169 604.0
19 TraesCS1D01G452100 chrUn 86.501 563 60 7 931 1491 320337585 320338133 2.770000e-169 604.0
20 TraesCS1D01G452100 chrUn 81.188 202 29 7 708 906 290639071 290638876 1.210000e-33 154.0
21 TraesCS1D01G452100 chrUn 81.188 202 29 7 708 906 290644796 290644601 1.210000e-33 154.0
22 TraesCS1D01G452100 chrUn 81.188 202 29 7 708 906 320337393 320337588 1.210000e-33 154.0
23 TraesCS1D01G452100 chr7A 94.737 114 6 0 2405 2518 727235234 727235347 7.160000e-41 178.0
24 TraesCS1D01G452100 chr7A 92.308 117 9 0 2402 2518 727240036 727240152 1.550000e-37 167.0
25 TraesCS1D01G452100 chr7A 91.358 81 7 0 2405 2485 653395148 653395068 7.360000e-21 111.0
26 TraesCS1D01G452100 chr2D 93.103 116 7 1 2403 2518 639888039 639888153 4.310000e-38 169.0
27 TraesCS1D01G452100 chr3A 92.308 117 9 0 2402 2518 727208438 727208554 1.550000e-37 167.0
28 TraesCS1D01G452100 chr3A 91.304 115 10 0 2404 2518 727203618 727203732 9.320000e-35 158.0


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 TraesCS1D01G452100 chr1D 493781024 493783541 2517 True 4650.00 4650 100.0000 1 2518 1 chr1D.!!$R2 2517
1 TraesCS1D01G452100 chr1D 494306796 494307502 706 False 632.00 632 83.1750 931 1651 1 chr1D.!!$F2 720
2 TraesCS1D01G452100 chr1D 494349692 494350237 545 False 603.00 603 86.4770 930 1491 1 chr1D.!!$F3 561
3 TraesCS1D01G452100 chr1A 592098804 592101243 2439 True 1523.00 2185 89.9975 18 2400 2 chr1A.!!$R1 2382
4 TraesCS1D01G452100 chr1A 592994122 592994813 691 False 400.50 643 86.7180 753 1491 2 chr1A.!!$F3 738
5 TraesCS1D01G452100 chr1B 687531409 687531956 547 False 616.00 616 86.8330 930 1491 1 chr1B.!!$F1 561
6 TraesCS1D01G452100 chr1B 686852521 686855051 2530 True 480.06 1206 89.0158 1 2341 5 chr1B.!!$R1 2340
7 TraesCS1D01G452100 chrUn 290638331 290639071 740 True 379.00 604 83.8445 708 1491 2 chrUn.!!$R1 783
8 TraesCS1D01G452100 chrUn 290644056 290644796 740 True 379.00 604 83.8445 708 1491 2 chrUn.!!$R2 783
9 TraesCS1D01G452100 chrUn 320337393 320338133 740 False 379.00 604 83.8445 708 1491 2 chrUn.!!$F1 783

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
389 406 0.036388 TGACCGATCAAGGAAGTGGC 60.036 55.0 0.0 0.0 34.73 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 2209 0.254178 ATCGAGCCAATTCAGCAGGT 59.746 50.0 0.0 0.0 0.0 4.0 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 4.566426 CTCTCCTCCCTCTGTTTTTCAT 57.434 45.455 0.00 0.00 0.00 2.57
22 23 4.512484 CTCTCCTCCCTCTGTTTTTCATC 58.488 47.826 0.00 0.00 0.00 2.92
25 33 5.073691 TCTCCTCCCTCTGTTTTTCATCTTT 59.926 40.000 0.00 0.00 0.00 2.52
115 123 3.432517 GCTAGAGGCAGGCGATATG 57.567 57.895 0.00 0.00 41.35 1.78
162 170 5.508567 TCCTGATTGGTTTTGATCTATGCA 58.491 37.500 0.00 0.00 37.07 3.96
166 174 4.439305 TTGGTTTTGATCTATGCAGCAC 57.561 40.909 0.00 0.00 0.00 4.40
206 214 5.503002 TGCAGCCATGTATATGCATCTATT 58.497 37.500 0.19 0.00 43.34 1.73
207 215 5.947566 TGCAGCCATGTATATGCATCTATTT 59.052 36.000 0.19 0.00 43.34 1.40
258 267 4.082026 GCCTTTTTGTGCTTATCCTCATGT 60.082 41.667 0.00 0.00 0.00 3.21
260 269 5.047802 CCTTTTTGTGCTTATCCTCATGTGT 60.048 40.000 0.00 0.00 0.00 3.72
338 348 5.831103 TCCTTGATCTTATCTTTTGCCCTT 58.169 37.500 0.00 0.00 0.00 3.95
378 395 4.038522 TCTCTGATCTTTCCATGACCGATC 59.961 45.833 0.00 1.06 0.00 3.69
389 406 0.036388 TGACCGATCAAGGAAGTGGC 60.036 55.000 0.00 0.00 34.73 5.01
408 425 1.807142 GCAGACACCAACTAAGAAGGC 59.193 52.381 0.00 0.00 0.00 4.35
441 458 2.221169 CCTCTTGCAACAGCAGTTACA 58.779 47.619 0.00 0.00 39.82 2.41
448 465 4.245660 TGCAACAGCAGTTACATACTCTC 58.754 43.478 0.00 0.00 35.85 3.20
494 511 7.721399 TCTTAATTTGTTTCTTCTGCCTCTCTT 59.279 33.333 0.00 0.00 0.00 2.85
498 515 4.636249 TGTTTCTTCTGCCTCTCTTTCTC 58.364 43.478 0.00 0.00 0.00 2.87
500 517 4.799564 TTCTTCTGCCTCTCTTTCTCTC 57.200 45.455 0.00 0.00 0.00 3.20
501 518 4.046286 TCTTCTGCCTCTCTTTCTCTCT 57.954 45.455 0.00 0.00 0.00 3.10
502 519 4.415596 TCTTCTGCCTCTCTTTCTCTCTT 58.584 43.478 0.00 0.00 0.00 2.85
504 521 6.013379 TCTTCTGCCTCTCTTTCTCTCTTTA 58.987 40.000 0.00 0.00 0.00 1.85
505 522 5.652994 TCTGCCTCTCTTTCTCTCTTTAC 57.347 43.478 0.00 0.00 0.00 2.01
570 591 4.469945 TCCCTGGTTACAAGATCGAGATTT 59.530 41.667 0.00 0.00 0.00 2.17
571 592 5.045869 TCCCTGGTTACAAGATCGAGATTTT 60.046 40.000 0.00 0.00 0.00 1.82
633 655 7.063074 GCTGATTTATAATTTGGATCTGCATGC 59.937 37.037 11.82 11.82 39.76 4.06
728 863 7.416022 CAGATTCTTTTTGTCCTCATCTATGC 58.584 38.462 0.00 0.00 0.00 3.14
739 874 3.199508 CCTCATCTATGCAATCTAGGGGG 59.800 52.174 0.00 0.00 0.00 5.40
922 1234 6.710597 ACGTGTGCTTATCTTCCTATTAGA 57.289 37.500 0.00 0.00 0.00 2.10
923 1235 6.505272 ACGTGTGCTTATCTTCCTATTAGAC 58.495 40.000 0.00 0.00 0.00 2.59
1094 1407 2.412065 GCAATCAGTTTCACTGCGAGAC 60.412 50.000 0.00 0.00 45.54 3.36
1161 1474 2.793232 GGGCAACACGTTCGATATAGTC 59.207 50.000 0.00 0.00 39.74 2.59
1221 1544 8.713737 CGGAGGTACTTACTTTAGCTAATTTT 57.286 34.615 7.08 0.00 41.55 1.82
1222 1545 9.159364 CGGAGGTACTTACTTTAGCTAATTTTT 57.841 33.333 7.08 0.00 41.55 1.94
1283 1611 4.102054 ACATACTGCATGATCACCTCATCA 59.898 41.667 0.00 0.00 42.91 3.07
1294 1622 7.558161 TGATCACCTCATCAACACAATATTC 57.442 36.000 0.00 0.00 29.41 1.75
1296 1624 4.875536 TCACCTCATCAACACAATATTCCG 59.124 41.667 0.00 0.00 0.00 4.30
1371 1699 1.135139 CTGATGTGAAGATCGTCGGGT 59.865 52.381 4.15 0.00 0.00 5.28
1376 1704 0.109458 TGAAGATCGTCGGGTTGTCG 60.109 55.000 4.15 0.00 0.00 4.35
1382 1710 1.804326 CGTCGGGTTGTCGGATGAC 60.804 63.158 0.00 0.00 45.71 3.06
1506 1834 3.512033 AGAAGCTAGAACAGTTAGCGG 57.488 47.619 0.00 0.00 46.29 5.52
1560 1902 4.644498 TGCATAAAGCTAGCTCATATGCA 58.356 39.130 40.49 40.49 46.85 3.96
1561 1903 5.250982 TGCATAAAGCTAGCTCATATGCAT 58.749 37.500 40.49 19.69 45.71 3.96
1657 2013 6.347725 GCGTGATTAGCAAGAAGAAGAAGAAA 60.348 38.462 0.00 0.00 34.19 2.52
1659 2015 8.070171 CGTGATTAGCAAGAAGAAGAAGAAAAA 58.930 33.333 0.00 0.00 0.00 1.94
1660 2016 9.392021 GTGATTAGCAAGAAGAAGAAGAAAAAG 57.608 33.333 0.00 0.00 0.00 2.27
1661 2017 8.078596 TGATTAGCAAGAAGAAGAAGAAAAAGC 58.921 33.333 0.00 0.00 0.00 3.51
1662 2018 5.841957 AGCAAGAAGAAGAAGAAAAAGCA 57.158 34.783 0.00 0.00 0.00 3.91
1663 2019 5.829829 AGCAAGAAGAAGAAGAAAAAGCAG 58.170 37.500 0.00 0.00 0.00 4.24
1664 2020 4.443725 GCAAGAAGAAGAAGAAAAAGCAGC 59.556 41.667 0.00 0.00 0.00 5.25
1665 2021 5.585390 CAAGAAGAAGAAGAAAAAGCAGCA 58.415 37.500 0.00 0.00 0.00 4.41
1666 2022 5.435820 AGAAGAAGAAGAAAAAGCAGCAG 57.564 39.130 0.00 0.00 0.00 4.24
1667 2023 3.639716 AGAAGAAGAAAAAGCAGCAGC 57.360 42.857 0.00 0.00 42.56 5.25
1668 2024 2.954318 AGAAGAAGAAAAAGCAGCAGCA 59.046 40.909 3.17 0.00 45.49 4.41
1669 2025 3.004524 AGAAGAAGAAAAAGCAGCAGCAG 59.995 43.478 3.17 0.00 45.49 4.24
1670 2026 1.000496 AGAAGAAAAAGCAGCAGCAGC 60.000 47.619 3.17 0.46 45.49 5.25
1671 2027 0.748450 AAGAAAAAGCAGCAGCAGCA 59.252 45.000 12.92 0.00 45.49 4.41
1672 2028 0.314302 AGAAAAAGCAGCAGCAGCAG 59.686 50.000 12.92 0.00 45.49 4.24
1714 2070 9.435688 CGACATAATTAGACCATTTGGATGATA 57.564 33.333 3.01 0.00 38.94 2.15
1749 2105 6.808008 ATTGTCATTTGGATCGGATGATAC 57.192 37.500 0.00 0.00 35.84 2.24
1809 2165 2.625823 GGAATGTGGCCACGTGGTG 61.626 63.158 33.92 11.99 37.57 4.17
1821 2182 0.318107 ACGTGGTGCACAGTACGTAC 60.318 55.000 31.09 18.10 46.50 3.67
1822 2183 1.332180 CGTGGTGCACAGTACGTACG 61.332 60.000 23.66 15.01 33.40 3.67
1823 2184 0.318107 GTGGTGCACAGTACGTACGT 60.318 55.000 25.98 25.98 34.08 3.57
1824 2185 1.069296 GTGGTGCACAGTACGTACGTA 60.069 52.381 23.60 23.60 34.08 3.57
1909 2271 4.503370 GTCGATCTACAAAGTTTCGGATCC 59.497 45.833 0.00 0.00 33.34 3.36
1924 2286 1.002684 GGATCCAGCGAGTACAGTACG 60.003 57.143 6.95 0.00 0.00 3.67
1925 2287 1.669779 GATCCAGCGAGTACAGTACGT 59.330 52.381 5.02 0.00 0.00 3.57
1926 2288 2.385013 TCCAGCGAGTACAGTACGTA 57.615 50.000 5.02 0.00 0.00 3.57
2038 2418 1.859398 CGTACACACGCTGCACAAT 59.141 52.632 0.00 0.00 42.05 2.71
2048 2428 3.620300 CTGCACAATGCCAGCCACG 62.620 63.158 0.00 0.00 44.23 4.94
2052 2432 1.674322 ACAATGCCAGCCACGTACC 60.674 57.895 0.00 0.00 0.00 3.34
2143 2523 2.431057 GCCAACTAGCTAGCCAAGTCTA 59.569 50.000 20.91 0.48 0.00 2.59
2144 2524 3.738590 GCCAACTAGCTAGCCAAGTCTAC 60.739 52.174 20.91 8.70 0.00 2.59
2145 2525 3.702045 CCAACTAGCTAGCCAAGTCTACT 59.298 47.826 20.91 3.10 0.00 2.57
2158 2586 4.118410 CAAGTCTACTCCATGAGACATGC 58.882 47.826 13.12 0.00 43.81 4.06
2223 2655 4.248859 CGATCCATCTTGTCACTTCAAGT 58.751 43.478 6.38 0.00 43.44 3.16
2233 2665 3.243501 TGTCACTTCAAGTGGTACGTACC 60.244 47.826 33.42 33.42 45.94 3.34
2392 2836 7.324935 TGTATGCTTCCTCGAAAACTTACATA 58.675 34.615 0.00 0.00 0.00 2.29
2400 2844 8.420374 TCCTCGAAAACTTACATAATCATCAC 57.580 34.615 0.00 0.00 0.00 3.06
2401 2845 7.494625 TCCTCGAAAACTTACATAATCATCACC 59.505 37.037 0.00 0.00 0.00 4.02
2402 2846 7.254795 CCTCGAAAACTTACATAATCATCACCC 60.255 40.741 0.00 0.00 0.00 4.61
2403 2847 6.540914 TCGAAAACTTACATAATCATCACCCC 59.459 38.462 0.00 0.00 0.00 4.95
2404 2848 6.542370 CGAAAACTTACATAATCATCACCCCT 59.458 38.462 0.00 0.00 0.00 4.79
2405 2849 7.713507 CGAAAACTTACATAATCATCACCCCTA 59.286 37.037 0.00 0.00 0.00 3.53
2406 2850 9.574516 GAAAACTTACATAATCATCACCCCTAT 57.425 33.333 0.00 0.00 0.00 2.57
2407 2851 9.936329 AAAACTTACATAATCATCACCCCTATT 57.064 29.630 0.00 0.00 0.00 1.73
2410 2854 8.826765 ACTTACATAATCATCACCCCTATTAGG 58.173 37.037 2.43 2.43 34.30 2.69
2411 2855 8.751215 TTACATAATCATCACCCCTATTAGGT 57.249 34.615 8.91 0.00 38.48 3.08
2412 2856 7.648177 ACATAATCATCACCCCTATTAGGTT 57.352 36.000 8.91 0.00 34.56 3.50
2413 2857 7.461749 ACATAATCATCACCCCTATTAGGTTG 58.538 38.462 8.91 5.75 34.56 3.77
2414 2858 7.294720 ACATAATCATCACCCCTATTAGGTTGA 59.705 37.037 8.91 10.52 34.56 3.18
2415 2859 6.786843 AATCATCACCCCTATTAGGTTGAT 57.213 37.500 14.33 14.33 36.73 2.57
2416 2860 5.825593 TCATCACCCCTATTAGGTTGATC 57.174 43.478 16.15 0.00 35.28 2.92
2417 2861 4.283467 TCATCACCCCTATTAGGTTGATCG 59.717 45.833 16.15 13.08 35.28 3.69
2418 2862 3.918566 TCACCCCTATTAGGTTGATCGA 58.081 45.455 8.91 0.00 34.56 3.59
2419 2863 4.489737 TCACCCCTATTAGGTTGATCGAT 58.510 43.478 8.91 0.00 34.56 3.59
2420 2864 4.283467 TCACCCCTATTAGGTTGATCGATG 59.717 45.833 0.54 0.00 34.56 3.84
2421 2865 3.583086 ACCCCTATTAGGTTGATCGATGG 59.417 47.826 0.54 0.00 32.05 3.51
2422 2866 3.838317 CCCCTATTAGGTTGATCGATGGA 59.162 47.826 0.54 0.00 31.93 3.41
2423 2867 4.286032 CCCCTATTAGGTTGATCGATGGAA 59.714 45.833 0.54 0.00 31.93 3.53
2424 2868 5.482908 CCCTATTAGGTTGATCGATGGAAG 58.517 45.833 0.54 0.00 31.93 3.46
2425 2869 4.932200 CCTATTAGGTTGATCGATGGAAGC 59.068 45.833 0.54 5.22 0.00 3.86
2440 2884 2.882324 GGAAGCGTTCCTACTCTTCAG 58.118 52.381 9.42 0.00 44.26 3.02
2441 2885 2.417515 GGAAGCGTTCCTACTCTTCAGG 60.418 54.545 9.42 0.00 44.26 3.86
2442 2886 1.187087 AGCGTTCCTACTCTTCAGGG 58.813 55.000 0.00 0.00 33.66 4.45
2443 2887 0.175989 GCGTTCCTACTCTTCAGGGG 59.824 60.000 0.00 0.00 33.66 4.79
2444 2888 0.824759 CGTTCCTACTCTTCAGGGGG 59.175 60.000 0.00 0.00 33.66 5.40
2445 2889 1.618888 CGTTCCTACTCTTCAGGGGGA 60.619 57.143 0.00 0.00 33.66 4.81
2446 2890 2.112190 GTTCCTACTCTTCAGGGGGAG 58.888 57.143 0.00 0.00 33.66 4.30
2447 2891 1.695065 TCCTACTCTTCAGGGGGAGA 58.305 55.000 0.00 0.00 33.66 3.71
2448 2892 1.571457 TCCTACTCTTCAGGGGGAGAG 59.429 57.143 0.00 0.00 33.66 3.20
2449 2893 1.408969 CTACTCTTCAGGGGGAGAGC 58.591 60.000 0.00 0.00 34.11 4.09
2450 2894 0.032017 TACTCTTCAGGGGGAGAGCC 60.032 60.000 0.00 0.00 34.11 4.70
2451 2895 2.364317 TCTTCAGGGGGAGAGCCG 60.364 66.667 0.00 0.00 33.83 5.52
2452 2896 4.168291 CTTCAGGGGGAGAGCCGC 62.168 72.222 0.00 0.00 45.88 6.53
2459 2903 4.143333 GGGAGAGCCGCGTTGCTA 62.143 66.667 9.91 0.00 42.95 3.49
2460 2904 2.107141 GGAGAGCCGCGTTGCTAT 59.893 61.111 9.91 7.04 42.95 2.97
2461 2905 1.362717 GGAGAGCCGCGTTGCTATA 59.637 57.895 9.91 0.00 42.95 1.31
2462 2906 0.038159 GGAGAGCCGCGTTGCTATAT 60.038 55.000 9.91 0.00 42.95 0.86
2463 2907 1.201647 GGAGAGCCGCGTTGCTATATA 59.798 52.381 9.91 0.00 42.95 0.86
2464 2908 2.159226 GGAGAGCCGCGTTGCTATATAT 60.159 50.000 9.91 0.00 42.95 0.86
2465 2909 3.512680 GAGAGCCGCGTTGCTATATATT 58.487 45.455 9.91 0.00 42.95 1.28
2466 2910 3.254060 AGAGCCGCGTTGCTATATATTG 58.746 45.455 9.91 0.00 42.95 1.90
2467 2911 3.056821 AGAGCCGCGTTGCTATATATTGA 60.057 43.478 9.91 0.00 42.95 2.57
2468 2912 3.861840 AGCCGCGTTGCTATATATTGAT 58.138 40.909 8.16 0.00 40.56 2.57
2469 2913 3.618594 AGCCGCGTTGCTATATATTGATG 59.381 43.478 8.16 0.00 40.56 3.07
2470 2914 3.785505 GCCGCGTTGCTATATATTGATGC 60.786 47.826 4.92 0.00 0.00 3.91
2471 2915 3.542097 CCGCGTTGCTATATATTGATGCG 60.542 47.826 4.92 12.37 41.32 4.73
2472 2916 3.542097 CGCGTTGCTATATATTGATGCGG 60.542 47.826 0.00 0.00 38.34 5.69
2473 2917 3.616821 GCGTTGCTATATATTGATGCGGA 59.383 43.478 0.00 0.00 0.00 5.54
2474 2918 4.492570 GCGTTGCTATATATTGATGCGGAC 60.493 45.833 0.00 0.00 0.00 4.79
2475 2919 4.625311 CGTTGCTATATATTGATGCGGACA 59.375 41.667 0.00 0.00 0.00 4.02
2476 2920 5.220284 CGTTGCTATATATTGATGCGGACAG 60.220 44.000 0.00 0.00 0.00 3.51
2477 2921 5.659440 TGCTATATATTGATGCGGACAGA 57.341 39.130 0.00 0.00 0.00 3.41
2478 2922 6.036577 TGCTATATATTGATGCGGACAGAA 57.963 37.500 0.00 0.00 0.00 3.02
2479 2923 6.101997 TGCTATATATTGATGCGGACAGAAG 58.898 40.000 0.00 0.00 0.00 2.85
2480 2924 6.071391 TGCTATATATTGATGCGGACAGAAGA 60.071 38.462 0.00 0.00 0.00 2.87
2481 2925 6.254589 GCTATATATTGATGCGGACAGAAGAC 59.745 42.308 0.00 0.00 0.00 3.01
2482 2926 2.029838 ATTGATGCGGACAGAAGACC 57.970 50.000 0.00 0.00 0.00 3.85
2483 2927 0.976641 TTGATGCGGACAGAAGACCT 59.023 50.000 0.00 0.00 0.00 3.85
2496 2940 5.562506 CAGAAGACCTGTCGTAGATTACA 57.437 43.478 0.00 0.00 40.67 2.41
2497 2941 5.950883 CAGAAGACCTGTCGTAGATTACAA 58.049 41.667 0.00 0.00 40.67 2.41
2498 2942 6.030849 CAGAAGACCTGTCGTAGATTACAAG 58.969 44.000 0.00 0.00 40.67 3.16
2499 2943 5.944599 AGAAGACCTGTCGTAGATTACAAGA 59.055 40.000 0.00 0.00 40.67 3.02
2500 2944 5.564048 AGACCTGTCGTAGATTACAAGAC 57.436 43.478 0.00 0.00 40.67 3.01
2501 2945 5.008331 AGACCTGTCGTAGATTACAAGACA 58.992 41.667 0.00 0.00 40.67 3.41
2505 2949 5.306532 TGTCGTAGATTACAAGACAGGAC 57.693 43.478 0.00 0.00 40.67 3.85
2506 2950 4.142752 TGTCGTAGATTACAAGACAGGACG 60.143 45.833 0.00 0.00 40.67 4.79
2507 2951 4.093998 GTCGTAGATTACAAGACAGGACGA 59.906 45.833 0.00 0.00 40.67 4.20
2508 2952 4.880120 TCGTAGATTACAAGACAGGACGAT 59.120 41.667 0.00 0.00 32.39 3.73
2509 2953 5.007430 TCGTAGATTACAAGACAGGACGATC 59.993 44.000 0.00 0.00 32.39 3.69
2510 2954 4.294416 AGATTACAAGACAGGACGATCG 57.706 45.455 14.88 14.88 0.00 3.69
2511 2955 2.273370 TTACAAGACAGGACGATCGC 57.727 50.000 16.60 8.04 0.00 4.58
2512 2956 1.460504 TACAAGACAGGACGATCGCT 58.539 50.000 16.60 1.60 0.00 4.93
2513 2957 1.460504 ACAAGACAGGACGATCGCTA 58.539 50.000 16.60 0.00 0.00 4.26
2514 2958 1.402259 ACAAGACAGGACGATCGCTAG 59.598 52.381 16.60 5.45 0.00 3.42
2515 2959 1.025812 AAGACAGGACGATCGCTAGG 58.974 55.000 16.60 5.44 0.00 3.02
2516 2960 0.180642 AGACAGGACGATCGCTAGGA 59.819 55.000 16.60 0.00 0.00 2.94
2517 2961 1.202830 AGACAGGACGATCGCTAGGAT 60.203 52.381 16.60 0.00 38.35 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 33 2.715046 AGATGCATGGCGAGAGAAAAA 58.285 42.857 2.46 0.00 0.00 1.94
71 79 9.894783 CAAATTAATCTCCATCAATCATGTCTC 57.105 33.333 0.00 0.00 0.00 3.36
106 114 4.765273 TGTTTCACATGTACATATCGCCT 58.235 39.130 8.32 0.00 0.00 5.52
107 115 5.478233 TTGTTTCACATGTACATATCGCC 57.522 39.130 8.32 0.00 0.00 5.54
108 116 4.963953 GCTTGTTTCACATGTACATATCGC 59.036 41.667 8.32 0.00 0.00 4.58
109 117 6.349973 AGCTTGTTTCACATGTACATATCG 57.650 37.500 8.32 0.00 0.00 2.92
115 123 4.213270 TGCACTAGCTTGTTTCACATGTAC 59.787 41.667 0.00 0.00 42.74 2.90
162 170 1.408702 ACAGCAACCAAAAATCGTGCT 59.591 42.857 0.00 0.00 0.00 4.40
166 174 2.200067 TGCAACAGCAACCAAAAATCG 58.800 42.857 0.00 0.00 34.85 3.34
258 267 1.795872 CGACATGTAGCACCGAAAACA 59.204 47.619 0.00 0.00 0.00 2.83
260 269 0.793861 GCGACATGTAGCACCGAAAA 59.206 50.000 23.92 0.00 0.00 2.29
316 325 5.680665 GCAAGGGCAAAAGATAAGATCAAGG 60.681 44.000 0.00 0.00 40.72 3.61
334 344 7.330208 CAGAGAAAAGAAATTTGTATGCAAGGG 59.670 37.037 0.00 0.00 35.82 3.95
338 348 9.017509 AGATCAGAGAAAAGAAATTTGTATGCA 57.982 29.630 0.00 0.00 34.49 3.96
378 395 0.179020 TGGTGTCTGCCACTTCCTTG 60.179 55.000 0.00 0.00 43.94 3.61
389 406 2.069273 CGCCTTCTTAGTTGGTGTCTG 58.931 52.381 0.00 0.00 0.00 3.51
399 416 1.138047 CGCACGTACCGCCTTCTTAG 61.138 60.000 0.00 0.00 0.00 2.18
441 458 8.489676 AGGAACAGATACAATCATGAGAGTAT 57.510 34.615 17.84 17.84 0.00 2.12
522 539 8.620116 AGCCAAATTAAAAATAGTGCAACATT 57.380 26.923 0.00 0.00 41.43 2.71
570 591 3.078097 TGTTTAGGCAGCGCATCTAAAA 58.922 40.909 22.20 10.80 35.56 1.52
571 592 2.418628 GTGTTTAGGCAGCGCATCTAAA 59.581 45.455 11.47 16.54 32.56 1.85
607 628 7.063074 GCATGCAGATCCAAATTATAAATCAGC 59.937 37.037 14.21 5.12 31.73 4.26
633 655 4.619973 ACAACAACCAGTGCAACAATATG 58.380 39.130 0.00 0.00 41.43 1.78
739 874 4.079500 AGGGGAAGAGATGGAGATTTTTCC 60.080 45.833 0.00 0.00 37.77 3.13
740 875 4.886489 CAGGGGAAGAGATGGAGATTTTTC 59.114 45.833 0.00 0.00 0.00 2.29
922 1234 8.083828 AGTTATTTCTGATCCACATCTACTGT 57.916 34.615 0.00 0.00 39.20 3.55
988 1301 1.077123 GATGCCATGATCAGCTAGCG 58.923 55.000 9.55 4.60 0.00 4.26
1283 1611 6.811253 AACATGTACACGGAATATTGTGTT 57.189 33.333 14.63 0.00 46.61 3.32
1294 1622 7.354025 TGTCAAGTAATTAACATGTACACGG 57.646 36.000 0.00 0.00 0.00 4.94
1296 1624 7.094975 TGCCTGTCAAGTAATTAACATGTACAC 60.095 37.037 0.00 0.00 0.00 2.90
1506 1834 2.101770 GCTGGATCAAGCAAGCGC 59.898 61.111 17.67 0.00 43.01 5.92
1560 1902 3.028850 AGTGCATGCCAAAAGCTATGAT 58.971 40.909 16.68 0.00 44.23 2.45
1561 1903 2.449464 AGTGCATGCCAAAAGCTATGA 58.551 42.857 16.68 0.00 44.23 2.15
1664 2020 2.047179 TCTCTGCTGCTGCTGCTG 60.047 61.111 27.67 26.32 40.48 4.41
1665 2021 2.266372 CTCTCTGCTGCTGCTGCT 59.734 61.111 27.67 0.00 40.48 4.24
1666 2022 2.820479 CCTCTCTGCTGCTGCTGC 60.820 66.667 22.51 22.51 40.48 5.25
1667 2023 1.957765 TAGCCTCTCTGCTGCTGCTG 61.958 60.000 17.00 15.94 42.77 4.41
1668 2024 1.685077 TAGCCTCTCTGCTGCTGCT 60.685 57.895 17.00 2.30 42.77 4.24
1669 2025 1.521234 GTAGCCTCTCTGCTGCTGC 60.521 63.158 8.89 8.89 42.77 5.25
1670 2026 1.143620 GGTAGCCTCTCTGCTGCTG 59.856 63.158 0.00 0.00 42.73 4.41
1671 2027 2.422231 CGGTAGCCTCTCTGCTGCT 61.422 63.158 0.00 0.00 42.73 4.24
1672 2028 2.105930 CGGTAGCCTCTCTGCTGC 59.894 66.667 0.00 0.00 42.77 5.25
1673 2029 1.315981 TGTCGGTAGCCTCTCTGCTG 61.316 60.000 0.00 0.00 42.77 4.41
1831 2192 3.740141 GCAGGTAGGTAGGTACGTACGTA 60.740 52.174 23.60 23.60 44.25 3.57
1832 2193 2.906354 CAGGTAGGTAGGTACGTACGT 58.094 52.381 25.98 25.98 44.25 3.57
1833 2194 1.599542 GCAGGTAGGTAGGTACGTACG 59.400 57.143 18.98 15.01 44.25 3.67
1834 2195 2.615912 CAGCAGGTAGGTAGGTACGTAC 59.384 54.545 17.56 17.56 43.22 3.67
1835 2196 2.505407 TCAGCAGGTAGGTAGGTACGTA 59.495 50.000 0.00 0.00 0.00 3.57
1836 2197 1.283029 TCAGCAGGTAGGTAGGTACGT 59.717 52.381 0.00 0.00 0.00 3.57
1837 2198 2.048444 TCAGCAGGTAGGTAGGTACG 57.952 55.000 0.00 0.00 0.00 3.67
1838 2199 4.443034 CCAATTCAGCAGGTAGGTAGGTAC 60.443 50.000 0.00 0.00 0.00 3.34
1839 2200 3.709653 CCAATTCAGCAGGTAGGTAGGTA 59.290 47.826 0.00 0.00 0.00 3.08
1840 2201 2.505819 CCAATTCAGCAGGTAGGTAGGT 59.494 50.000 0.00 0.00 0.00 3.08
1841 2202 2.746472 GCCAATTCAGCAGGTAGGTAGG 60.746 54.545 0.00 0.00 0.00 3.18
1842 2203 2.171448 AGCCAATTCAGCAGGTAGGTAG 59.829 50.000 0.15 0.00 0.00 3.18
1843 2204 2.170607 GAGCCAATTCAGCAGGTAGGTA 59.829 50.000 0.15 0.00 0.00 3.08
1844 2205 0.995024 AGCCAATTCAGCAGGTAGGT 59.005 50.000 0.15 0.00 0.00 3.08
1845 2206 1.673168 GAGCCAATTCAGCAGGTAGG 58.327 55.000 0.15 0.00 0.00 3.18
1846 2207 1.134699 TCGAGCCAATTCAGCAGGTAG 60.135 52.381 0.15 0.00 0.00 3.18
1847 2208 0.901827 TCGAGCCAATTCAGCAGGTA 59.098 50.000 0.15 0.00 0.00 3.08
1848 2209 0.254178 ATCGAGCCAATTCAGCAGGT 59.746 50.000 0.00 0.00 0.00 4.00
1909 2271 3.302350 GCTACTACGTACTGTACTCGCTG 60.302 52.174 15.35 2.80 0.00 5.18
1924 2286 5.594724 ATCAAGTCGATCGTAGCTACTAC 57.405 43.478 21.20 11.07 33.99 2.73
1925 2287 6.253083 CGATATCAAGTCGATCGTAGCTACTA 59.747 42.308 21.20 11.48 41.40 1.82
1926 2288 5.062433 CGATATCAAGTCGATCGTAGCTACT 59.938 44.000 21.20 7.82 41.40 2.57
1995 2375 9.447040 CGTGATATAGAGAATAGAAACAAACGA 57.553 33.333 0.00 0.00 0.00 3.85
1996 2376 9.234384 ACGTGATATAGAGAATAGAAACAAACG 57.766 33.333 0.00 0.00 0.00 3.60
2048 2428 1.745653 GCGTATATAGGACGGGGGTAC 59.254 57.143 6.62 0.00 40.66 3.34
2052 2432 0.529378 GGTGCGTATATAGGACGGGG 59.471 60.000 6.62 0.00 40.66 5.73
2143 2523 0.986527 TGTGGCATGTCTCATGGAGT 59.013 50.000 10.96 0.00 0.00 3.85
2144 2524 1.947456 CATGTGGCATGTCTCATGGAG 59.053 52.381 26.99 8.64 35.47 3.86
2145 2525 2.020181 GCATGTGGCATGTCTCATGGA 61.020 52.381 32.11 2.49 43.97 3.41
2158 2586 7.310664 GGATTCAAATAGACATATGCATGTGG 58.689 38.462 24.94 9.98 45.58 4.17
2286 2725 4.165036 CGATTGCTAGGATTCATCTCGAG 58.835 47.826 5.93 5.93 0.00 4.04
2400 2844 3.838317 TCCATCGATCAACCTAATAGGGG 59.162 47.826 11.52 2.65 40.58 4.79
2401 2845 5.482908 CTTCCATCGATCAACCTAATAGGG 58.517 45.833 11.52 0.00 40.58 3.53
2402 2846 4.932200 GCTTCCATCGATCAACCTAATAGG 59.068 45.833 4.46 4.46 42.49 2.57
2403 2847 4.623167 CGCTTCCATCGATCAACCTAATAG 59.377 45.833 0.00 0.00 0.00 1.73
2404 2848 4.038763 ACGCTTCCATCGATCAACCTAATA 59.961 41.667 0.00 0.00 0.00 0.98
2405 2849 3.181465 ACGCTTCCATCGATCAACCTAAT 60.181 43.478 0.00 0.00 0.00 1.73
2406 2850 2.167693 ACGCTTCCATCGATCAACCTAA 59.832 45.455 0.00 0.00 0.00 2.69
2407 2851 1.754803 ACGCTTCCATCGATCAACCTA 59.245 47.619 0.00 0.00 0.00 3.08
2408 2852 0.537188 ACGCTTCCATCGATCAACCT 59.463 50.000 0.00 0.00 0.00 3.50
2409 2853 1.327764 GAACGCTTCCATCGATCAACC 59.672 52.381 0.00 0.00 0.00 3.77
2410 2854 2.721129 GAACGCTTCCATCGATCAAC 57.279 50.000 0.00 0.00 0.00 3.18
2422 2866 1.550976 CCCTGAAGAGTAGGAACGCTT 59.449 52.381 0.00 0.00 46.80 4.68
2423 2867 1.187087 CCCTGAAGAGTAGGAACGCT 58.813 55.000 0.00 0.00 37.35 5.07
2424 2868 0.175989 CCCCTGAAGAGTAGGAACGC 59.824 60.000 0.00 0.00 37.52 4.84
2425 2869 0.824759 CCCCCTGAAGAGTAGGAACG 59.175 60.000 0.00 0.00 37.52 3.95
2426 2870 2.112190 CTCCCCCTGAAGAGTAGGAAC 58.888 57.143 0.00 0.00 37.52 3.62
2427 2871 2.008400 TCTCCCCCTGAAGAGTAGGAA 58.992 52.381 0.00 0.00 37.52 3.36
2428 2872 1.571457 CTCTCCCCCTGAAGAGTAGGA 59.429 57.143 0.00 0.00 37.52 2.94
2429 2873 2.032151 GCTCTCCCCCTGAAGAGTAGG 61.032 61.905 0.00 0.00 35.01 3.18
2430 2874 1.408969 GCTCTCCCCCTGAAGAGTAG 58.591 60.000 0.00 0.00 0.00 2.57
2431 2875 0.032017 GGCTCTCCCCCTGAAGAGTA 60.032 60.000 0.00 0.00 0.00 2.59
2432 2876 1.306568 GGCTCTCCCCCTGAAGAGT 60.307 63.158 0.00 0.00 0.00 3.24
2433 2877 2.430610 CGGCTCTCCCCCTGAAGAG 61.431 68.421 0.00 0.00 0.00 2.85
2434 2878 2.364317 CGGCTCTCCCCCTGAAGA 60.364 66.667 0.00 0.00 0.00 2.87
2435 2879 4.168291 GCGGCTCTCCCCCTGAAG 62.168 72.222 0.00 0.00 0.00 3.02
2442 2886 2.083835 TATAGCAACGCGGCTCTCCC 62.084 60.000 13.24 0.00 44.54 4.30
2443 2887 0.038159 ATATAGCAACGCGGCTCTCC 60.038 55.000 13.24 0.00 44.54 3.71
2444 2888 2.631418 TATATAGCAACGCGGCTCTC 57.369 50.000 13.24 0.00 44.54 3.20
2445 2889 3.056821 TCAATATATAGCAACGCGGCTCT 60.057 43.478 13.24 6.80 44.54 4.09
2446 2890 3.250744 TCAATATATAGCAACGCGGCTC 58.749 45.455 13.24 0.00 44.54 4.70
2448 2892 3.785505 GCATCAATATATAGCAACGCGGC 60.786 47.826 12.47 4.85 0.00 6.53
2449 2893 3.542097 CGCATCAATATATAGCAACGCGG 60.542 47.826 12.47 0.00 35.65 6.46
2450 2894 3.542097 CCGCATCAATATATAGCAACGCG 60.542 47.826 3.53 3.53 38.76 6.01
2451 2895 3.616821 TCCGCATCAATATATAGCAACGC 59.383 43.478 0.00 0.00 0.00 4.84
2452 2896 4.625311 TGTCCGCATCAATATATAGCAACG 59.375 41.667 0.00 0.00 0.00 4.10
2453 2897 5.869344 TCTGTCCGCATCAATATATAGCAAC 59.131 40.000 0.00 0.00 0.00 4.17
2454 2898 6.036577 TCTGTCCGCATCAATATATAGCAA 57.963 37.500 0.00 0.00 0.00 3.91
2455 2899 5.659440 TCTGTCCGCATCAATATATAGCA 57.341 39.130 0.00 0.00 0.00 3.49
2456 2900 6.254589 GTCTTCTGTCCGCATCAATATATAGC 59.745 42.308 0.00 0.00 0.00 2.97
2457 2901 6.754209 GGTCTTCTGTCCGCATCAATATATAG 59.246 42.308 0.00 0.00 0.00 1.31
2458 2902 6.437477 AGGTCTTCTGTCCGCATCAATATATA 59.563 38.462 0.00 0.00 0.00 0.86
2459 2903 5.247110 AGGTCTTCTGTCCGCATCAATATAT 59.753 40.000 0.00 0.00 0.00 0.86
2460 2904 4.588951 AGGTCTTCTGTCCGCATCAATATA 59.411 41.667 0.00 0.00 0.00 0.86
2461 2905 3.389329 AGGTCTTCTGTCCGCATCAATAT 59.611 43.478 0.00 0.00 0.00 1.28
2462 2906 2.766263 AGGTCTTCTGTCCGCATCAATA 59.234 45.455 0.00 0.00 0.00 1.90
2463 2907 1.556911 AGGTCTTCTGTCCGCATCAAT 59.443 47.619 0.00 0.00 0.00 2.57
2464 2908 0.976641 AGGTCTTCTGTCCGCATCAA 59.023 50.000 0.00 0.00 0.00 2.57
2465 2909 0.247460 CAGGTCTTCTGTCCGCATCA 59.753 55.000 0.00 0.00 38.64 3.07
2466 2910 3.056628 CAGGTCTTCTGTCCGCATC 57.943 57.895 0.00 0.00 38.64 3.91
2475 2919 5.944599 TCTTGTAATCTACGACAGGTCTTCT 59.055 40.000 0.00 0.00 0.00 2.85
2476 2920 6.028987 GTCTTGTAATCTACGACAGGTCTTC 58.971 44.000 0.00 0.00 0.00 2.87
2477 2921 5.475909 TGTCTTGTAATCTACGACAGGTCTT 59.524 40.000 0.00 0.00 31.62 3.01
2478 2922 5.008331 TGTCTTGTAATCTACGACAGGTCT 58.992 41.667 0.00 0.00 31.62 3.85
2479 2923 5.306532 TGTCTTGTAATCTACGACAGGTC 57.693 43.478 0.00 0.00 31.62 3.85
2480 2924 5.312120 CTGTCTTGTAATCTACGACAGGT 57.688 43.478 9.25 0.00 44.69 4.00
2482 2926 5.333513 GTCCTGTCTTGTAATCTACGACAG 58.666 45.833 9.97 9.97 46.76 3.51
2483 2927 4.142752 CGTCCTGTCTTGTAATCTACGACA 60.143 45.833 0.00 0.00 33.94 4.35
2484 2928 4.093998 TCGTCCTGTCTTGTAATCTACGAC 59.906 45.833 0.00 0.00 32.52 4.34
2485 2929 4.256110 TCGTCCTGTCTTGTAATCTACGA 58.744 43.478 0.00 0.00 34.80 3.43
2486 2930 4.611310 TCGTCCTGTCTTGTAATCTACG 57.389 45.455 0.00 0.00 0.00 3.51
2487 2931 5.206299 CGATCGTCCTGTCTTGTAATCTAC 58.794 45.833 7.03 0.00 0.00 2.59
2488 2932 4.261072 GCGATCGTCCTGTCTTGTAATCTA 60.261 45.833 17.81 0.00 0.00 1.98
2489 2933 3.489398 GCGATCGTCCTGTCTTGTAATCT 60.489 47.826 17.81 0.00 0.00 2.40
2490 2934 2.789893 GCGATCGTCCTGTCTTGTAATC 59.210 50.000 17.81 0.00 0.00 1.75
2491 2935 2.427453 AGCGATCGTCCTGTCTTGTAAT 59.573 45.455 17.81 0.00 0.00 1.89
2492 2936 1.816835 AGCGATCGTCCTGTCTTGTAA 59.183 47.619 17.81 0.00 0.00 2.41
2493 2937 1.460504 AGCGATCGTCCTGTCTTGTA 58.539 50.000 17.81 0.00 0.00 2.41
2494 2938 1.402259 CTAGCGATCGTCCTGTCTTGT 59.598 52.381 17.81 0.00 0.00 3.16
2495 2939 1.268794 CCTAGCGATCGTCCTGTCTTG 60.269 57.143 17.81 4.95 0.00 3.02
2496 2940 1.025812 CCTAGCGATCGTCCTGTCTT 58.974 55.000 17.81 0.00 0.00 3.01
2497 2941 0.180642 TCCTAGCGATCGTCCTGTCT 59.819 55.000 17.81 6.44 0.00 3.41
2498 2942 1.240256 ATCCTAGCGATCGTCCTGTC 58.760 55.000 17.81 0.00 0.00 3.51
2499 2943 3.423344 ATCCTAGCGATCGTCCTGT 57.577 52.632 17.81 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.