Multiple sequence alignment - TraesCS2B01G087200

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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 TraesCS2B01G087200 chr2B 100.000 2945 0 0 1 2945 49295015 49297959 0.000000e+00 5439.0
1 TraesCS2B01G087200 chr2B 91.760 716 35 12 1 699 48137743 48137035 0.000000e+00 974.0
2 TraesCS2B01G087200 chr2B 83.803 142 15 8 1261 1396 385191179 385191318 8.570000e-26 128.0
3 TraesCS2B01G087200 chr6B 93.383 1345 42 11 696 2021 54078031 54079347 0.000000e+00 1947.0
4 TraesCS2B01G087200 chr6B 97.778 585 13 0 2361 2945 54080499 54081083 0.000000e+00 1009.0
5 TraesCS2B01G087200 chr6B 85.686 510 46 12 2361 2844 316611936 316612444 2.020000e-141 512.0
6 TraesCS2B01G087200 chr6B 98.718 234 3 0 2076 2309 54079368 54079601 1.630000e-112 416.0
7 TraesCS2B01G087200 chr6B 83.934 361 41 6 2602 2945 663565632 663565272 2.190000e-86 329.0
8 TraesCS2B01G087200 chr2A 90.720 625 32 14 1 606 32013014 32012397 0.000000e+00 809.0
9 TraesCS2B01G087200 chr2A 82.217 433 39 22 1484 1885 327153914 327153489 3.640000e-89 339.0
10 TraesCS2B01G087200 chr2A 86.096 187 14 2 2758 2932 598464245 598464059 1.080000e-44 191.0
11 TraesCS2B01G087200 chr2A 85.034 147 10 2 2758 2892 603915010 603914864 3.960000e-29 139.0
12 TraesCS2B01G087200 chr2A 93.333 90 6 0 1932 2021 474289034 474289123 1.840000e-27 134.0
13 TraesCS2B01G087200 chr2A 81.250 128 16 4 985 1109 755378048 755378170 2.420000e-16 97.1
14 TraesCS2B01G087200 chr6A 87.022 601 56 7 2361 2940 576229025 576228426 0.000000e+00 658.0
15 TraesCS2B01G087200 chr6A 86.855 601 57 7 2361 2940 576400955 576400356 0.000000e+00 652.0
16 TraesCS2B01G087200 chr6A 83.372 433 34 19 1484 1885 458200031 458199606 1.670000e-97 366.0
17 TraesCS2B01G087200 chr6A 86.972 284 35 2 1197 1479 458200474 458200192 4.740000e-83 318.0
18 TraesCS2B01G087200 chr6A 79.343 213 23 12 918 1109 2970523 2970311 2.380000e-26 130.0
19 TraesCS2B01G087200 chr6A 79.343 213 23 12 918 1109 107697305 107697517 2.380000e-26 130.0
20 TraesCS2B01G087200 chr5B 86.634 606 59 7 2361 2945 237132280 237132884 0.000000e+00 651.0
21 TraesCS2B01G087200 chr3B 83.372 433 34 19 1484 1885 795061238 795060813 1.670000e-97 366.0
22 TraesCS2B01G087200 chr3B 87.324 284 34 2 1197 1479 65166231 65165949 1.020000e-84 324.0
23 TraesCS2B01G087200 chr3B 87.273 275 33 2 1197 1470 795061680 795061407 2.200000e-81 313.0
24 TraesCS2B01G087200 chr3B 78.873 213 24 12 918 1109 145891239 145891027 1.110000e-24 124.0
25 TraesCS2B01G087200 chr1B 83.372 433 34 19 1484 1885 106359438 106359013 1.670000e-97 366.0
26 TraesCS2B01G087200 chr1B 90.000 70 7 0 994 1063 84414974 84414905 1.120000e-14 91.6
27 TraesCS2B01G087200 chr1B 91.111 45 4 0 2454 2498 394035074 394035118 8.810000e-06 62.1
28 TraesCS2B01G087200 chr1A 83.372 433 34 19 1484 1885 77465440 77465015 1.670000e-97 366.0
29 TraesCS2B01G087200 chr1A 86.268 284 37 2 1197 1479 77465883 77465601 1.030000e-79 307.0
30 TraesCS2B01G087200 chr7A 83.372 433 33 20 1484 1885 679115181 679114757 6.000000e-97 364.0
31 TraesCS2B01G087200 chr7A 86.268 284 37 2 1197 1479 679115624 679115342 1.030000e-79 307.0
32 TraesCS2B01G087200 chr7A 79.343 213 23 12 918 1109 110075117 110075329 2.380000e-26 130.0
33 TraesCS2B01G087200 chr7A 93.333 45 3 0 2454 2498 95895555 95895599 1.890000e-07 67.6
34 TraesCS2B01G087200 chr7A 93.333 45 3 0 2454 2498 95903857 95903901 1.890000e-07 67.6
35 TraesCS2B01G087200 chr7A 100.000 28 0 0 1860 1887 315507281 315507308 5.000000e-03 52.8
36 TraesCS2B01G087200 chr4B 82.910 433 35 20 1484 1885 192723411 192722987 1.300000e-93 353.0
37 TraesCS2B01G087200 chr4B 85.563 284 39 2 1197 1479 192723854 192723572 2.220000e-76 296.0
38 TraesCS2B01G087200 chr3A 82.910 433 35 20 1484 1885 732559373 732559797 1.300000e-93 353.0
39 TraesCS2B01G087200 chr3A 85.614 285 39 2 1197 1480 732558930 732559213 6.170000e-77 298.0
40 TraesCS2B01G087200 chr3A 94.444 90 5 0 1932 2021 164423042 164422953 3.960000e-29 139.0
41 TraesCS2B01G087200 chr7B 88.356 146 9 7 287 428 680224071 680224212 5.050000e-38 169.0
42 TraesCS2B01G087200 chr1D 87.619 105 7 3 2396 2498 476113991 476114091 1.850000e-22 117.0
43 TraesCS2B01G087200 chr1D 77.465 213 27 10 918 1109 45060474 45060686 1.120000e-19 108.0
44 TraesCS2B01G087200 chr5D 82.400 125 16 2 987 1105 160751114 160751238 1.440000e-18 104.0


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 TraesCS2B01G087200 chr2B 49295015 49297959 2944 False 5439.0 5439 100.000000 1 2945 1 chr2B.!!$F1 2944
1 TraesCS2B01G087200 chr2B 48137035 48137743 708 True 974.0 974 91.760000 1 699 1 chr2B.!!$R1 698
2 TraesCS2B01G087200 chr6B 54078031 54081083 3052 False 1124.0 1947 96.626333 696 2945 3 chr6B.!!$F2 2249
3 TraesCS2B01G087200 chr6B 316611936 316612444 508 False 512.0 512 85.686000 2361 2844 1 chr6B.!!$F1 483
4 TraesCS2B01G087200 chr2A 32012397 32013014 617 True 809.0 809 90.720000 1 606 1 chr2A.!!$R1 605
5 TraesCS2B01G087200 chr6A 576228426 576229025 599 True 658.0 658 87.022000 2361 2940 1 chr6A.!!$R2 579
6 TraesCS2B01G087200 chr6A 576400356 576400955 599 True 652.0 652 86.855000 2361 2940 1 chr6A.!!$R3 579
7 TraesCS2B01G087200 chr6A 458199606 458200474 868 True 342.0 366 85.172000 1197 1885 2 chr6A.!!$R4 688
8 TraesCS2B01G087200 chr5B 237132280 237132884 604 False 651.0 651 86.634000 2361 2945 1 chr5B.!!$F1 584
9 TraesCS2B01G087200 chr3B 795060813 795061680 867 True 339.5 366 85.322500 1197 1885 2 chr3B.!!$R3 688
10 TraesCS2B01G087200 chr1A 77465015 77465883 868 True 336.5 366 84.820000 1197 1885 2 chr1A.!!$R1 688
11 TraesCS2B01G087200 chr7A 679114757 679115624 867 True 335.5 364 84.820000 1197 1885 2 chr7A.!!$R1 688
12 TraesCS2B01G087200 chr4B 192722987 192723854 867 True 324.5 353 84.236500 1197 1885 2 chr4B.!!$R1 688
13 TraesCS2B01G087200 chr3A 732558930 732559797 867 False 325.5 353 84.262000 1197 1885 2 chr3A.!!$F1 688

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
741 763 0.669619 TCGCTTCTGGTTGTACGTCA 59.33 50.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2648 3735 1.064003 AACAGGTGGTGCAGTGGATA 58.936 50.0 0.0 0.0 0.0 2.59 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
232 233 5.365403 TGTTTAAGACATAAAAGGCACCG 57.635 39.130 0.00 0.00 35.33 4.94
242 249 3.552132 AAAAGGCACCGACCAATTTTT 57.448 38.095 0.00 0.00 0.00 1.94
304 312 4.523083 ACATATAGTGTGGCACGGAAAAT 58.477 39.130 13.77 4.75 40.28 1.82
459 474 8.966868 ACCACCACATAAAATCTACCATAAAAG 58.033 33.333 0.00 0.00 0.00 2.27
505 523 4.799949 CAGGCATCAAAAACATATTGTCGG 59.200 41.667 0.00 0.00 0.00 4.79
513 531 4.419522 AAACATATTGTCGGTGCAGAAC 57.580 40.909 0.00 0.00 0.00 3.01
585 607 8.117813 ACATAATTTTAGCCCATAATAACCCG 57.882 34.615 0.00 0.00 0.00 5.28
609 631 6.533723 CGCGGCATACCTATAAATATTTCTCA 59.466 38.462 3.39 0.00 0.00 3.27
610 632 7.224753 CGCGGCATACCTATAAATATTTCTCAT 59.775 37.037 3.39 0.00 0.00 2.90
611 633 8.552034 GCGGCATACCTATAAATATTTCTCATC 58.448 37.037 3.39 0.00 0.00 2.92
665 687 9.353999 GAACATTTTTGTCTCACTTAAACAGTT 57.646 29.630 0.00 0.00 30.92 3.16
668 690 9.520204 CATTTTTGTCTCACTTAAACAGTTCAT 57.480 29.630 0.00 0.00 30.92 2.57
692 714 5.648330 ACTCCTTAGAAACAGAAAAGGGT 57.352 39.130 0.00 0.00 39.21 4.34
693 715 5.622180 ACTCCTTAGAAACAGAAAAGGGTC 58.378 41.667 0.00 0.00 39.21 4.46
694 716 5.132144 ACTCCTTAGAAACAGAAAAGGGTCA 59.868 40.000 0.00 0.00 39.21 4.02
725 747 3.985925 CCTACTATTAAACCACGGATCGC 59.014 47.826 0.00 0.00 0.00 4.58
728 750 4.117685 ACTATTAAACCACGGATCGCTTC 58.882 43.478 0.00 0.00 0.00 3.86
732 754 1.827399 AACCACGGATCGCTTCTGGT 61.827 55.000 0.00 0.00 36.77 4.00
733 755 1.079127 CCACGGATCGCTTCTGGTT 60.079 57.895 0.00 0.00 34.77 3.67
741 763 0.669619 TCGCTTCTGGTTGTACGTCA 59.330 50.000 0.00 0.00 0.00 4.35
743 765 1.654105 CGCTTCTGGTTGTACGTCATC 59.346 52.381 0.00 0.00 0.00 2.92
746 768 3.770666 CTTCTGGTTGTACGTCATCGAT 58.229 45.455 0.00 0.00 40.62 3.59
747 769 3.145212 TCTGGTTGTACGTCATCGATG 57.855 47.619 19.61 19.61 40.62 3.84
758 780 3.684305 ACGTCATCGATGATTTTGCAGAA 59.316 39.130 29.53 1.57 39.30 3.02
775 797 5.686753 TGCAGAAAAGTCCCTACAGTTTTA 58.313 37.500 0.00 0.00 30.50 1.52
776 798 5.763204 TGCAGAAAAGTCCCTACAGTTTTAG 59.237 40.000 0.00 0.00 30.50 1.85
797 819 1.483415 GTATTCAACCCGCAGTCCCTA 59.517 52.381 0.00 0.00 0.00 3.53
800 837 1.153168 CAACCCGCAGTCCCTATGG 60.153 63.158 0.00 0.00 0.00 2.74
826 864 4.710528 ACGTTTCGTTTTTGCACAAAAA 57.289 31.818 15.40 15.40 44.98 1.94
1324 1366 0.976641 ACTGGCTGAAGGTCATTCGA 59.023 50.000 0.00 0.00 41.14 3.71
1483 1682 0.324923 TTCCCCGTCCTAGCAGCTAA 60.325 55.000 3.09 0.00 0.00 3.09
1549 1748 3.706594 TGCTACTTCTTCCCTACATCCTG 59.293 47.826 0.00 0.00 0.00 3.86
1558 1757 4.552883 TCCCTACATCCTGAAGGTATGA 57.447 45.455 12.76 0.00 36.34 2.15
1644 1847 0.250513 CCCTCCCTCTCGTTTCCTTG 59.749 60.000 0.00 0.00 0.00 3.61
1658 1878 4.516698 CGTTTCCTTGCAAGATATAGCCAT 59.483 41.667 28.05 0.00 0.00 4.40
1659 1879 5.009010 CGTTTCCTTGCAAGATATAGCCATT 59.991 40.000 28.05 0.00 0.00 3.16
1806 2038 5.748402 TCAGATGTCACCTTTATTGCTGAT 58.252 37.500 0.00 0.00 0.00 2.90
2017 2249 6.925718 TGTTGGAGAATCAGATCGATGAATAC 59.074 38.462 0.54 0.00 36.25 1.89
2021 2253 7.014615 TGGAGAATCAGATCGATGAATACTGAA 59.985 37.037 15.28 3.00 40.21 3.02
2022 2254 7.328249 GGAGAATCAGATCGATGAATACTGAAC 59.672 40.741 15.28 12.61 40.21 3.18
2024 2256 9.072375 AGAATCAGATCGATGAATACTGAACTA 57.928 33.333 15.28 0.00 40.21 2.24
2026 2258 9.689976 AATCAGATCGATGAATACTGAACTAAG 57.310 33.333 15.28 0.00 40.21 2.18
2027 2259 8.226819 TCAGATCGATGAATACTGAACTAAGT 57.773 34.615 0.54 0.00 35.20 2.24
2029 2261 8.750416 CAGATCGATGAATACTGAACTAAGTTG 58.250 37.037 0.54 0.00 0.00 3.16
2030 2262 6.887376 TCGATGAATACTGAACTAAGTTGC 57.113 37.500 0.00 0.00 0.00 4.17
2032 2264 6.310467 TCGATGAATACTGAACTAAGTTGCAC 59.690 38.462 0.00 0.00 0.00 4.57
2033 2265 5.839262 TGAATACTGAACTAAGTTGCACG 57.161 39.130 0.00 0.00 0.00 5.34
2035 2267 6.163476 TGAATACTGAACTAAGTTGCACGAT 58.837 36.000 0.00 0.00 0.00 3.73
2036 2268 6.649141 TGAATACTGAACTAAGTTGCACGATT 59.351 34.615 0.00 0.00 0.00 3.34
2037 2269 7.172532 TGAATACTGAACTAAGTTGCACGATTT 59.827 33.333 0.00 0.00 0.00 2.17
2038 2270 5.095691 ACTGAACTAAGTTGCACGATTTG 57.904 39.130 0.00 0.00 0.00 2.32
2039 2271 4.574828 ACTGAACTAAGTTGCACGATTTGT 59.425 37.500 0.00 0.00 0.00 2.83
2041 2273 4.814234 TGAACTAAGTTGCACGATTTGTCT 59.186 37.500 0.00 0.00 0.00 3.41
2042 2274 4.992381 ACTAAGTTGCACGATTTGTCTC 57.008 40.909 0.00 0.00 0.00 3.36
2043 2275 4.377021 ACTAAGTTGCACGATTTGTCTCA 58.623 39.130 0.00 0.00 0.00 3.27
2044 2276 4.997395 ACTAAGTTGCACGATTTGTCTCAT 59.003 37.500 0.00 0.00 0.00 2.90
2045 2277 3.818961 AGTTGCACGATTTGTCTCATG 57.181 42.857 0.00 0.00 0.00 3.07
2046 2278 3.402110 AGTTGCACGATTTGTCTCATGA 58.598 40.909 0.00 0.00 0.00 3.07
2047 2279 4.005650 AGTTGCACGATTTGTCTCATGAT 58.994 39.130 0.00 0.00 0.00 2.45
2048 2280 4.456911 AGTTGCACGATTTGTCTCATGATT 59.543 37.500 0.00 0.00 0.00 2.57
2049 2281 5.048504 AGTTGCACGATTTGTCTCATGATTT 60.049 36.000 0.00 0.00 0.00 2.17
2050 2282 5.375417 TGCACGATTTGTCTCATGATTTT 57.625 34.783 0.00 0.00 0.00 1.82
2051 2283 5.771469 TGCACGATTTGTCTCATGATTTTT 58.229 33.333 0.00 0.00 0.00 1.94
2052 2284 5.858049 TGCACGATTTGTCTCATGATTTTTC 59.142 36.000 0.00 0.00 0.00 2.29
2053 2285 5.858049 GCACGATTTGTCTCATGATTTTTCA 59.142 36.000 0.00 0.00 0.00 2.69
2054 2286 6.363088 GCACGATTTGTCTCATGATTTTTCAA 59.637 34.615 0.00 0.00 0.00 2.69
2055 2287 7.096106 GCACGATTTGTCTCATGATTTTTCAAA 60.096 33.333 0.00 4.87 0.00 2.69
2056 2288 8.754096 CACGATTTGTCTCATGATTTTTCAAAA 58.246 29.630 0.00 0.00 0.00 2.44
2057 2289 9.311916 ACGATTTGTCTCATGATTTTTCAAAAA 57.688 25.926 0.00 0.00 0.00 1.94
2061 2293 7.424227 TGTCTCATGATTTTTCAAAAATGGC 57.576 32.000 12.95 0.63 0.00 4.40
2062 2294 7.218614 TGTCTCATGATTTTTCAAAAATGGCT 58.781 30.769 12.95 0.00 0.00 4.75
2063 2295 7.716123 TGTCTCATGATTTTTCAAAAATGGCTT 59.284 29.630 12.95 0.00 0.00 4.35
2064 2296 8.562052 GTCTCATGATTTTTCAAAAATGGCTTT 58.438 29.630 12.95 0.00 0.00 3.51
2065 2297 9.775854 TCTCATGATTTTTCAAAAATGGCTTTA 57.224 25.926 12.95 0.00 0.00 1.85
2067 2299 9.775854 TCATGATTTTTCAAAAATGGCTTTAGA 57.224 25.926 12.95 0.00 0.00 2.10
2303 2535 3.777106 TCAATCTGCCTTCACTGAACT 57.223 42.857 0.00 0.00 0.00 3.01
2309 2541 3.065655 CTGCCTTCACTGAACTTCTGAG 58.934 50.000 2.88 0.00 0.00 3.35
2312 2544 2.805099 CCTTCACTGAACTTCTGAGCAC 59.195 50.000 2.88 0.00 0.00 4.40
2313 2545 3.494048 CCTTCACTGAACTTCTGAGCACT 60.494 47.826 2.88 0.00 0.00 4.40
2314 2546 4.262207 CCTTCACTGAACTTCTGAGCACTA 60.262 45.833 2.88 0.00 0.00 2.74
2315 2547 4.937201 TCACTGAACTTCTGAGCACTAA 57.063 40.909 2.88 0.00 0.00 2.24
2316 2548 4.621991 TCACTGAACTTCTGAGCACTAAC 58.378 43.478 2.88 0.00 0.00 2.34
2318 2550 4.210120 CACTGAACTTCTGAGCACTAACAC 59.790 45.833 2.88 0.00 0.00 3.32
2319 2551 4.100189 ACTGAACTTCTGAGCACTAACACT 59.900 41.667 2.88 0.00 0.00 3.55
2320 2552 4.371786 TGAACTTCTGAGCACTAACACTG 58.628 43.478 0.00 0.00 0.00 3.66
2321 2553 4.099419 TGAACTTCTGAGCACTAACACTGA 59.901 41.667 0.00 0.00 0.00 3.41
2322 2554 4.672587 ACTTCTGAGCACTAACACTGAA 57.327 40.909 0.00 0.00 0.00 3.02
2323 2555 4.372656 ACTTCTGAGCACTAACACTGAAC 58.627 43.478 0.00 0.00 0.00 3.18
2324 2556 4.100189 ACTTCTGAGCACTAACACTGAACT 59.900 41.667 0.00 0.00 0.00 3.01
2325 2557 4.672587 TCTGAGCACTAACACTGAACTT 57.327 40.909 0.00 0.00 0.00 2.66
2326 2558 4.621991 TCTGAGCACTAACACTGAACTTC 58.378 43.478 0.00 0.00 0.00 3.01
2329 2561 3.733337 AGCACTAACACTGAACTTCCTG 58.267 45.455 0.00 0.00 0.00 3.86
2333 2565 3.454812 ACTAACACTGAACTTCCTGGTGT 59.545 43.478 0.00 0.00 41.95 4.16
2335 2567 4.497291 AACACTGAACTTCCTGGTGTTA 57.503 40.909 16.49 0.00 45.35 2.41
2336 2568 4.497291 ACACTGAACTTCCTGGTGTTAA 57.503 40.909 7.56 1.49 37.80 2.01
2337 2569 5.048846 ACACTGAACTTCCTGGTGTTAAT 57.951 39.130 7.56 0.00 37.80 1.40
2339 2571 5.531287 ACACTGAACTTCCTGGTGTTAATTC 59.469 40.000 7.56 0.40 37.80 2.17
2341 2573 6.934645 CACTGAACTTCCTGGTGTTAATTCTA 59.065 38.462 7.56 0.00 0.00 2.10
2342 2574 6.935208 ACTGAACTTCCTGGTGTTAATTCTAC 59.065 38.462 7.56 0.00 0.00 2.59
2343 2575 6.235664 TGAACTTCCTGGTGTTAATTCTACC 58.764 40.000 7.56 0.00 35.05 3.18
2344 2576 5.175388 ACTTCCTGGTGTTAATTCTACCC 57.825 43.478 0.00 0.00 33.51 3.69
2347 2579 3.054655 TCCTGGTGTTAATTCTACCCTGC 60.055 47.826 0.00 0.00 33.51 4.85
2348 2580 3.308117 CCTGGTGTTAATTCTACCCTGCA 60.308 47.826 0.00 0.00 33.51 4.41
2350 2582 3.585289 TGGTGTTAATTCTACCCTGCAGA 59.415 43.478 17.39 0.00 33.51 4.26
2352 2584 4.395231 GGTGTTAATTCTACCCTGCAGAAC 59.605 45.833 17.39 8.70 34.96 3.01
2353 2585 5.246307 GTGTTAATTCTACCCTGCAGAACT 58.754 41.667 17.39 0.00 34.96 3.01
2354 2586 6.403878 GTGTTAATTCTACCCTGCAGAACTA 58.596 40.000 17.39 0.00 34.96 2.24
2356 2588 6.877322 TGTTAATTCTACCCTGCAGAACTAAC 59.123 38.462 17.39 12.00 41.58 2.34
2357 2589 5.499004 AATTCTACCCTGCAGAACTAACA 57.501 39.130 17.39 0.00 34.96 2.41
2358 2590 3.955650 TCTACCCTGCAGAACTAACAC 57.044 47.619 17.39 0.00 0.00 3.32
2359 2591 3.507411 TCTACCCTGCAGAACTAACACT 58.493 45.455 17.39 0.00 0.00 3.55
2377 3455 8.328758 ACTAACACTAATTGATTTCCATGAGGA 58.671 33.333 0.00 0.00 43.93 3.71
2599 3686 0.320374 TGTTGGTTAGGTCCAGCTCG 59.680 55.000 0.00 0.00 39.04 5.03
2648 3735 3.114668 GCATGTGCAGATCTCTCATCT 57.885 47.619 0.00 0.00 41.59 2.90
2763 3853 2.110011 ACAGTTCCAAGGCCCAACTAAT 59.890 45.455 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
211 212 5.388111 GTCGGTGCCTTTTATGTCTTAAAC 58.612 41.667 0.00 0.00 29.47 2.01
212 213 4.456566 GGTCGGTGCCTTTTATGTCTTAAA 59.543 41.667 0.00 0.00 0.00 1.52
304 312 0.322366 TGATGGTCGCATGGCTCAAA 60.322 50.000 0.00 0.00 0.00 2.69
362 370 9.421806 CTTATGGCATTTTTCTTAATGTTGTGA 57.578 29.630 4.78 0.00 37.72 3.58
459 474 9.274065 CCTGAAGATACGCTAAAATGTTTAAAC 57.726 33.333 11.54 11.54 0.00 2.01
469 484 4.400529 TGATGCCTGAAGATACGCTAAA 57.599 40.909 0.00 0.00 0.00 1.85
470 485 4.400529 TTGATGCCTGAAGATACGCTAA 57.599 40.909 0.00 0.00 0.00 3.09
472 487 2.988010 TTGATGCCTGAAGATACGCT 57.012 45.000 0.00 0.00 0.00 5.07
473 488 4.098416 GTTTTTGATGCCTGAAGATACGC 58.902 43.478 0.00 0.00 0.00 4.42
570 592 1.072505 CCGCGGGTTATTATGGGCT 59.927 57.895 20.10 0.00 0.00 5.19
585 607 7.843490 TGAGAAATATTTATAGGTATGCCGC 57.157 36.000 0.00 0.00 40.50 6.53
622 644 9.927668 AAAAATGTTCCATAAACTATGTCAAGG 57.072 29.630 0.00 0.00 38.76 3.61
665 687 7.883311 CCCTTTTCTGTTTCTAAGGAGTAATGA 59.117 37.037 0.00 0.00 39.60 2.57
668 690 7.145474 ACCCTTTTCTGTTTCTAAGGAGTAA 57.855 36.000 0.00 0.00 39.60 2.24
682 704 8.487028 AGTAGGTAAAGATATGACCCTTTTCTG 58.513 37.037 0.00 0.00 34.74 3.02
710 732 2.343101 CAGAAGCGATCCGTGGTTTAA 58.657 47.619 0.00 0.00 0.00 1.52
719 741 1.278238 CGTACAACCAGAAGCGATCC 58.722 55.000 0.00 0.00 0.00 3.36
725 747 3.211803 TCGATGACGTACAACCAGAAG 57.788 47.619 0.00 0.00 40.69 2.85
728 750 3.145212 TCATCGATGACGTACAACCAG 57.855 47.619 23.99 0.00 40.69 4.00
732 754 4.390297 TGCAAAATCATCGATGACGTACAA 59.610 37.500 29.49 12.16 40.03 2.41
733 755 3.929610 TGCAAAATCATCGATGACGTACA 59.070 39.130 29.49 19.92 40.03 2.90
741 763 5.393461 GGGACTTTTCTGCAAAATCATCGAT 60.393 40.000 0.00 0.00 30.91 3.59
743 765 4.082571 AGGGACTTTTCTGCAAAATCATCG 60.083 41.667 0.00 0.00 27.25 3.84
746 768 5.136828 TGTAGGGACTTTTCTGCAAAATCA 58.863 37.500 0.00 0.00 41.75 2.57
747 769 5.241728 ACTGTAGGGACTTTTCTGCAAAATC 59.758 40.000 0.00 0.00 41.75 2.17
758 780 7.981142 TGAATACCTAAAACTGTAGGGACTTT 58.019 34.615 3.44 0.00 44.44 2.66
775 797 0.252197 GGACTGCGGGTTGAATACCT 59.748 55.000 0.00 0.00 46.86 3.08
776 798 0.746923 GGGACTGCGGGTTGAATACC 60.747 60.000 0.00 0.00 46.99 2.73
826 864 4.332828 GCAATAGACCAAACTACAGGGTT 58.667 43.478 0.00 0.00 34.39 4.11
832 870 1.669265 GCGGGCAATAGACCAAACTAC 59.331 52.381 0.00 0.00 46.60 2.73
917 958 2.510012 TTCTGCATCGAGCTGCCG 60.510 61.111 8.46 2.52 45.94 5.69
918 959 2.806856 CGTTCTGCATCGAGCTGCC 61.807 63.158 8.46 2.35 45.94 4.85
919 960 2.699809 CGTTCTGCATCGAGCTGC 59.300 61.111 4.01 4.01 45.94 5.25
920 961 2.806856 GCCGTTCTGCATCGAGCTG 61.807 63.158 0.00 7.61 45.94 4.24
921 962 2.510238 GCCGTTCTGCATCGAGCT 60.510 61.111 7.47 0.00 45.94 4.09
922 963 3.918220 CGCCGTTCTGCATCGAGC 61.918 66.667 7.47 0.00 45.96 5.03
923 964 3.257561 CCGCCGTTCTGCATCGAG 61.258 66.667 7.47 2.59 0.00 4.04
926 967 3.869272 CTGCCGCCGTTCTGCATC 61.869 66.667 0.00 0.00 34.41 3.91
1165 1206 3.414700 CAAGAACTTCGCGCCGCT 61.415 61.111 7.78 0.00 0.00 5.52
1301 1343 0.036010 ATGACCTTCAGCCAGTTCCG 60.036 55.000 0.00 0.00 0.00 4.30
1324 1366 1.198713 AGGCATGAAGTCGAGGATGT 58.801 50.000 0.00 0.00 0.00 3.06
1483 1682 2.043227 GCTGGGAGTAGCATAAGTCCT 58.957 52.381 7.34 0.00 43.17 3.85
1549 1748 7.838884 AGAGGTAGTGTAAGTTTCATACCTTC 58.161 38.462 16.91 12.77 42.29 3.46
1558 1757 4.262506 GGTGCAGAGAGGTAGTGTAAGTTT 60.263 45.833 0.00 0.00 0.00 2.66
1644 1847 7.483307 TCTCAACAAAAATGGCTATATCTTGC 58.517 34.615 0.00 0.00 0.00 4.01
1658 1878 6.148948 CCGCACATTTATCTCTCAACAAAAA 58.851 36.000 0.00 0.00 0.00 1.94
1659 1879 5.698832 CCGCACATTTATCTCTCAACAAAA 58.301 37.500 0.00 0.00 0.00 2.44
1801 2021 5.643664 TGCATCAAACATTAACTCATCAGC 58.356 37.500 0.00 0.00 0.00 4.26
1806 2038 4.832266 AGGGTTGCATCAAACATTAACTCA 59.168 37.500 0.00 0.00 31.89 3.41
2017 2249 5.050091 AGACAAATCGTGCAACTTAGTTCAG 60.050 40.000 0.00 0.00 31.75 3.02
2021 2253 4.377021 TGAGACAAATCGTGCAACTTAGT 58.623 39.130 0.00 0.00 31.75 2.24
2022 2254 4.990543 TGAGACAAATCGTGCAACTTAG 57.009 40.909 0.00 0.00 31.75 2.18
2024 2256 3.814842 TCATGAGACAAATCGTGCAACTT 59.185 39.130 0.00 0.00 36.37 2.66
2026 2258 3.811722 TCATGAGACAAATCGTGCAAC 57.188 42.857 0.00 0.00 36.37 4.17
2027 2259 5.375417 AAATCATGAGACAAATCGTGCAA 57.625 34.783 0.09 0.00 36.37 4.08
2029 2261 5.858049 TGAAAAATCATGAGACAAATCGTGC 59.142 36.000 0.09 0.00 36.37 5.34
2030 2262 7.856492 TTGAAAAATCATGAGACAAATCGTG 57.144 32.000 0.09 0.00 37.52 4.35
2035 2267 8.344098 GCCATTTTTGAAAAATCATGAGACAAA 58.656 29.630 12.58 6.52 0.00 2.83
2036 2268 7.716123 AGCCATTTTTGAAAAATCATGAGACAA 59.284 29.630 12.58 0.62 0.00 3.18
2037 2269 7.218614 AGCCATTTTTGAAAAATCATGAGACA 58.781 30.769 12.58 0.00 0.00 3.41
2038 2270 7.662604 AGCCATTTTTGAAAAATCATGAGAC 57.337 32.000 12.58 0.00 0.00 3.36
2039 2271 8.680039 AAAGCCATTTTTGAAAAATCATGAGA 57.320 26.923 12.58 0.00 0.00 3.27
2041 2273 9.775854 TCTAAAGCCATTTTTGAAAAATCATGA 57.224 25.926 12.58 0.00 29.54 3.07
2093 2325 5.046520 AGGTTAACAGGGTGTCAGATTAGAC 60.047 44.000 8.10 0.00 38.99 2.59
2281 2513 4.660168 AGTTCAGTGAAGGCAGATTGAAT 58.340 39.130 5.62 0.00 0.00 2.57
2303 2535 4.672587 AGTTCAGTGTTAGTGCTCAGAA 57.327 40.909 0.00 0.00 0.00 3.02
2309 2541 2.808543 CCAGGAAGTTCAGTGTTAGTGC 59.191 50.000 5.01 0.00 0.00 4.40
2312 2544 4.073293 ACACCAGGAAGTTCAGTGTTAG 57.927 45.455 15.79 4.21 38.47 2.34
2313 2545 4.497291 AACACCAGGAAGTTCAGTGTTA 57.503 40.909 24.94 0.00 46.69 2.41
2314 2546 3.366052 AACACCAGGAAGTTCAGTGTT 57.634 42.857 22.54 22.54 44.51 3.32
2315 2547 4.497291 TTAACACCAGGAAGTTCAGTGT 57.503 40.909 15.79 15.79 43.21 3.55
2316 2548 5.765182 AGAATTAACACCAGGAAGTTCAGTG 59.235 40.000 14.79 14.79 34.61 3.66
2318 2550 6.371825 GGTAGAATTAACACCAGGAAGTTCAG 59.628 42.308 5.01 0.00 32.32 3.02
2319 2551 6.235664 GGTAGAATTAACACCAGGAAGTTCA 58.764 40.000 5.01 0.00 32.32 3.18
2320 2552 5.646793 GGGTAGAATTAACACCAGGAAGTTC 59.353 44.000 0.00 0.00 33.78 3.01
2321 2553 5.312443 AGGGTAGAATTAACACCAGGAAGTT 59.688 40.000 0.00 0.00 33.78 2.66
2322 2554 4.850386 AGGGTAGAATTAACACCAGGAAGT 59.150 41.667 0.00 0.00 33.78 3.01
2323 2555 5.186198 CAGGGTAGAATTAACACCAGGAAG 58.814 45.833 0.00 0.00 33.78 3.46
2324 2556 4.566907 GCAGGGTAGAATTAACACCAGGAA 60.567 45.833 0.00 0.00 33.78 3.36
2325 2557 3.054655 GCAGGGTAGAATTAACACCAGGA 60.055 47.826 0.00 0.00 33.78 3.86
2326 2558 3.279434 GCAGGGTAGAATTAACACCAGG 58.721 50.000 5.29 0.00 33.78 4.45
2329 2561 4.216411 TCTGCAGGGTAGAATTAACACC 57.784 45.455 15.13 0.00 0.00 4.16
2333 2565 6.877322 GTGTTAGTTCTGCAGGGTAGAATTAA 59.123 38.462 15.13 5.29 36.63 1.40
2335 2567 5.013183 AGTGTTAGTTCTGCAGGGTAGAATT 59.987 40.000 15.13 0.00 36.63 2.17
2336 2568 4.532521 AGTGTTAGTTCTGCAGGGTAGAAT 59.467 41.667 15.13 0.00 36.63 2.40
2337 2569 3.901844 AGTGTTAGTTCTGCAGGGTAGAA 59.098 43.478 15.13 0.00 32.08 2.10
2339 2571 3.963428 AGTGTTAGTTCTGCAGGGTAG 57.037 47.619 15.13 0.00 0.00 3.18
2341 2573 4.910458 ATTAGTGTTAGTTCTGCAGGGT 57.090 40.909 15.13 0.98 0.00 4.34
2342 2574 5.245531 TCAATTAGTGTTAGTTCTGCAGGG 58.754 41.667 15.13 0.00 0.00 4.45
2343 2575 6.992063 ATCAATTAGTGTTAGTTCTGCAGG 57.008 37.500 15.13 0.00 0.00 4.85
2344 2576 7.965107 GGAAATCAATTAGTGTTAGTTCTGCAG 59.035 37.037 7.63 7.63 0.00 4.41
2347 2579 9.778993 CATGGAAATCAATTAGTGTTAGTTCTG 57.221 33.333 0.00 0.00 0.00 3.02
2348 2580 9.739276 TCATGGAAATCAATTAGTGTTAGTTCT 57.261 29.630 0.00 0.00 0.00 3.01
2350 2582 8.960591 CCTCATGGAAATCAATTAGTGTTAGTT 58.039 33.333 0.00 0.00 34.57 2.24
2352 2584 8.737168 TCCTCATGGAAATCAATTAGTGTTAG 57.263 34.615 0.00 0.00 39.87 2.34
2549 3636 2.348666 CCAAAGACGTTCTAATCTGCCG 59.651 50.000 0.00 0.00 0.00 5.69
2599 3686 1.746991 GCTAGGTCCAGTGCCAAGC 60.747 63.158 0.00 0.00 0.00 4.01
2648 3735 1.064003 AACAGGTGGTGCAGTGGATA 58.936 50.000 0.00 0.00 0.00 2.59
2763 3853 4.021916 GGGCTAAGAGTTGTGGTAGACTA 58.978 47.826 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.