Multiple sequence alignment - TraesCS1A01G306600

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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 TraesCS1A01G306600 chr1A 100.000 2798 0 0 1 2798 498598572 498595775 0.000000e+00 5168.0
1 TraesCS1A01G306600 chr1A 88.780 713 79 1 1085 1796 566564264 566564976 0.000000e+00 872.0
2 TraesCS1A01G306600 chr1D 91.745 1805 95 28 440 2225 403336694 403334925 0.000000e+00 2459.0
3 TraesCS1A01G306600 chr1D 86.658 802 104 3 998 1796 472560918 472561719 0.000000e+00 885.0
4 TraesCS1A01G306600 chr1D 95.455 242 11 0 200 441 403336971 403336730 1.220000e-103 387.0
5 TraesCS1A01G306600 chr1D 92.063 189 13 2 1 188 403337210 403337023 5.940000e-67 265.0
6 TraesCS1A01G306600 chr1D 92.424 66 4 1 30 95 30076122 30076058 2.970000e-15 93.5
7 TraesCS1A01G306600 chr1D 91.045 67 3 3 30 95 29814128 29814192 1.380000e-13 87.9
8 TraesCS1A01G306600 chr1D 94.286 35 2 0 2241 2275 3633207 3633241 1.000000e-03 54.7
9 TraesCS1A01G306600 chr1D 100.000 29 0 0 2247 2275 5082608 5082580 1.000000e-03 54.7
10 TraesCS1A01G306600 chr1B 90.994 1610 98 30 440 2012 542580541 542578942 0.000000e+00 2126.0
11 TraesCS1A01G306600 chr1B 89.781 1595 88 29 619 2193 542432876 542431337 0.000000e+00 1973.0
12 TraesCS1A01G306600 chr1B 88.780 713 79 1 1085 1796 657272156 657272868 0.000000e+00 872.0
13 TraesCS1A01G306600 chr1B 97.521 242 6 0 200 441 542580818 542580577 5.580000e-112 414.0
14 TraesCS1A01G306600 chr1B 90.114 263 20 4 2275 2535 542431326 542431068 1.240000e-88 337.0
15 TraesCS1A01G306600 chr1B 92.553 188 13 1 2 188 542581057 542580870 4.590000e-68 268.0
16 TraesCS1A01G306600 chr1B 83.219 292 12 10 2538 2798 542431019 542430734 1.680000e-57 233.0
17 TraesCS1A01G306600 chr5B 89.212 723 78 0 1076 1798 532876737 532877459 0.000000e+00 904.0
18 TraesCS1A01G306600 chr5A 88.520 723 83 0 1076 1798 553420966 553421688 0.000000e+00 876.0
19 TraesCS1A01G306600 chr5D 88.382 723 84 0 1076 1798 438360055 438360777 0.000000e+00 870.0
20 TraesCS1A01G306600 chr6B 88.931 262 19 7 1 252 117323858 117323597 5.820000e-82 315.0
21 TraesCS1A01G306600 chr6B 95.960 99 4 0 343 441 117318313 117318215 8.020000e-36 161.0
22 TraesCS1A01G306600 chr6B 87.129 101 7 4 89 188 117317237 117317142 2.950000e-20 110.0
23 TraesCS1A01G306600 chr3A 100.000 38 0 0 2196 2233 550510695 550510658 1.390000e-08 71.3
24 TraesCS1A01G306600 chr7B 95.122 41 2 0 2195 2235 449502779 449502739 6.470000e-07 65.8
25 TraesCS1A01G306600 chr2D 95.122 41 2 0 2195 2235 566557925 566557885 6.470000e-07 65.8
26 TraesCS1A01G306600 chr3D 95.000 40 2 0 2196 2235 105124419 105124458 2.330000e-06 63.9
27 TraesCS1A01G306600 chr6D 100.000 31 0 0 2239 2269 319006089 319006059 1.080000e-04 58.4


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 TraesCS1A01G306600 chr1A 498595775 498598572 2797 True 5168.000000 5168 100.000000 1 2798 1 chr1A.!!$R1 2797
1 TraesCS1A01G306600 chr1A 566564264 566564976 712 False 872.000000 872 88.780000 1085 1796 1 chr1A.!!$F1 711
2 TraesCS1A01G306600 chr1D 403334925 403337210 2285 True 1037.000000 2459 93.087667 1 2225 3 chr1D.!!$R3 2224
3 TraesCS1A01G306600 chr1D 472560918 472561719 801 False 885.000000 885 86.658000 998 1796 1 chr1D.!!$F3 798
4 TraesCS1A01G306600 chr1B 542578942 542581057 2115 True 936.000000 2126 93.689333 2 2012 3 chr1B.!!$R2 2010
5 TraesCS1A01G306600 chr1B 657272156 657272868 712 False 872.000000 872 88.780000 1085 1796 1 chr1B.!!$F1 711
6 TraesCS1A01G306600 chr1B 542430734 542432876 2142 True 847.666667 1973 87.704667 619 2798 3 chr1B.!!$R1 2179
7 TraesCS1A01G306600 chr5B 532876737 532877459 722 False 904.000000 904 89.212000 1076 1798 1 chr5B.!!$F1 722
8 TraesCS1A01G306600 chr5A 553420966 553421688 722 False 876.000000 876 88.520000 1076 1798 1 chr5A.!!$F1 722
9 TraesCS1A01G306600 chr5D 438360055 438360777 722 False 870.000000 870 88.382000 1076 1798 1 chr5D.!!$F1 722

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
784 870 0.110509 CACGTAAGCACAGCAAGCAG 60.111 55.0 0.0 0.0 45.62 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 1925 0.323633 CATGCATCCCAAGTCCCACA 60.324 55.0 0.0 0.0 0.0 4.17 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 5.834169 TGCGATTCATGAATGCATACAAAT 58.166 33.333 27.23 6.13 33.36 2.32
68 69 5.120208 TGTTTCTGCTAGTTTCAGCGAATAC 59.880 40.000 0.00 0.00 44.88 1.89
119 120 9.731819 TTCTTTACACGCAATTGTTATTTGTTA 57.268 25.926 7.40 0.00 0.00 2.41
168 169 7.471721 TCATTCTTTCAAATAATAGCGTGTGG 58.528 34.615 0.00 0.00 0.00 4.17
188 190 5.246656 TGTGGGATTGAATGCTGATTCTTTT 59.753 36.000 0.00 0.00 39.10 2.27
189 191 6.168389 GTGGGATTGAATGCTGATTCTTTTT 58.832 36.000 0.00 0.00 39.10 1.94
390 432 3.808726 TGAATGTGGCAAGATTTTTGTGC 59.191 39.130 0.00 0.00 37.55 4.57
429 471 9.090692 AGTTCTGAAAATTCTGACACAATTTTG 57.909 29.630 16.02 5.99 41.43 2.44
446 525 7.215789 ACAATTTTGTGGATGTAGCAATTTCA 58.784 30.769 0.00 0.00 40.49 2.69
451 530 3.509575 GTGGATGTAGCAATTTCACCCAA 59.490 43.478 0.00 0.00 0.00 4.12
463 542 7.338449 AGCAATTTCACCCAAGTTATATACGTT 59.662 33.333 0.00 0.00 0.00 3.99
464 543 7.971722 GCAATTTCACCCAAGTTATATACGTTT 59.028 33.333 0.00 0.00 0.00 3.60
503 582 5.888982 ACAGAGGGAGTAGAACAGAAAAA 57.111 39.130 0.00 0.00 0.00 1.94
512 591 6.127980 GGAGTAGAACAGAAAAATAGCAACCC 60.128 42.308 0.00 0.00 0.00 4.11
597 677 3.758554 GCCTGAGAGTAATTCCTTTTGCA 59.241 43.478 0.00 0.00 0.00 4.08
670 753 2.553602 GTCATTTGACACCACAGCATCA 59.446 45.455 5.84 0.00 44.18 3.07
684 767 1.741706 AGCATCAAAGGATTGCACGAG 59.258 47.619 0.00 0.00 36.45 4.18
708 791 5.406780 GCGTTTCAAGATGGAGAATCGATAT 59.593 40.000 0.00 0.00 40.54 1.63
709 792 6.073548 GCGTTTCAAGATGGAGAATCGATATT 60.074 38.462 0.00 0.00 35.09 1.28
710 793 7.116376 GCGTTTCAAGATGGAGAATCGATATTA 59.884 37.037 0.00 0.00 32.37 0.98
723 809 3.937814 TCGATATTATGTCCACATGGCC 58.062 45.455 0.00 0.00 37.15 5.36
751 837 4.785453 GGTTGCGCCCCTCTCTGG 62.785 72.222 4.18 0.00 0.00 3.86
784 870 0.110509 CACGTAAGCACAGCAAGCAG 60.111 55.000 0.00 0.00 45.62 4.24
863 949 1.425066 GATAGGCCCATCCATCCAACA 59.575 52.381 0.00 0.00 37.29 3.33
866 952 0.826062 GGCCCATCCATCCAACAAAG 59.174 55.000 0.00 0.00 34.01 2.77
893 986 4.335647 CCAGCAAGGCCCGTCAGT 62.336 66.667 0.00 0.00 0.00 3.41
940 1035 1.597742 GCTCTCTGCTTTCCACACAA 58.402 50.000 0.00 0.00 38.95 3.33
1008 1110 2.644418 GCAACTGCAATGGCGTCA 59.356 55.556 0.00 0.00 45.35 4.35
1071 1179 1.687368 GCCAAGATTGCCTCCTCCAAT 60.687 52.381 0.00 0.00 35.73 3.16
1182 1293 2.647875 CTCTATCTCGGCCCGCTG 59.352 66.667 0.00 0.00 0.00 5.18
1245 1356 2.603473 TACGGCTGGGACACTGCT 60.603 61.111 6.53 0.00 42.95 4.24
1290 1401 1.374758 CGCGAAGAACAGGGAGCTT 60.375 57.895 0.00 0.00 0.00 3.74
1557 1668 1.649815 GCTCGGTGAGATCGTCGAT 59.350 57.895 7.63 7.63 0.00 3.59
1590 1701 2.356780 CGGTAGCTTCGACCCCCTT 61.357 63.158 0.00 0.00 32.95 3.95
1650 1761 4.107072 AGGTGAAGGAGATCAAGAATGGA 58.893 43.478 0.00 0.00 0.00 3.41
1696 1807 0.250234 CTTCTTCGTCCAGGCCATCA 59.750 55.000 5.01 0.00 0.00 3.07
1710 1821 1.077501 CATCATCACCGGCAAGGGT 60.078 57.895 0.00 0.00 46.96 4.34
1830 1965 1.379044 CCTGTGGGACTTGGGATGC 60.379 63.158 0.00 0.00 33.58 3.91
2037 2177 3.820467 TCTGAAACAAATGCACAGTAGGG 59.180 43.478 0.00 0.00 0.00 3.53
2071 2211 0.247736 AAGAGCAGCCAAGGACTACG 59.752 55.000 0.00 0.00 0.00 3.51
2086 2226 6.651975 AGGACTACGAAAGAAGAAGAAGAA 57.348 37.500 0.00 0.00 0.00 2.52
2087 2227 6.683715 AGGACTACGAAAGAAGAAGAAGAAG 58.316 40.000 0.00 0.00 0.00 2.85
2088 2228 6.490721 AGGACTACGAAAGAAGAAGAAGAAGA 59.509 38.462 0.00 0.00 0.00 2.87
2089 2229 7.014422 AGGACTACGAAAGAAGAAGAAGAAGAA 59.986 37.037 0.00 0.00 0.00 2.52
2090 2230 7.327518 GGACTACGAAAGAAGAAGAAGAAGAAG 59.672 40.741 0.00 0.00 0.00 2.85
2091 2231 7.942990 ACTACGAAAGAAGAAGAAGAAGAAGA 58.057 34.615 0.00 0.00 0.00 2.87
2092 2232 8.414778 ACTACGAAAGAAGAAGAAGAAGAAGAA 58.585 33.333 0.00 0.00 0.00 2.52
2093 2233 7.707774 ACGAAAGAAGAAGAAGAAGAAGAAG 57.292 36.000 0.00 0.00 0.00 2.85
2110 2250 6.258899 AGAAGAAGAAAGAAAACAAACGAGC 58.741 36.000 0.00 0.00 0.00 5.03
2155 2295 4.576879 AGTAGCTGTACAACTTTAAGGCC 58.423 43.478 3.72 0.00 0.00 5.19
2193 2333 7.254227 TGGTTTAAGTCATTACAAGTGACAC 57.746 36.000 8.73 0.00 46.46 3.67
2196 2336 7.169645 GGTTTAAGTCATTACAAGTGACACGTA 59.830 37.037 8.73 0.00 46.46 3.57
2197 2337 7.627585 TTAAGTCATTACAAGTGACACGTAC 57.372 36.000 8.73 0.00 46.46 3.67
2207 2347 0.957395 TGACACGTACTCCCTCCGTC 60.957 60.000 0.00 0.00 31.46 4.79
2208 2348 0.676151 GACACGTACTCCCTCCGTCT 60.676 60.000 0.00 0.00 31.46 4.18
2222 2362 3.933332 CCTCCGTCTCAAAATGTAAGACC 59.067 47.826 0.00 0.00 36.84 3.85
2225 2365 5.556915 TCCGTCTCAAAATGTAAGACCATT 58.443 37.500 0.00 0.00 36.84 3.16
2226 2366 6.001460 TCCGTCTCAAAATGTAAGACCATTT 58.999 36.000 0.00 0.00 44.71 2.32
2236 2376 8.647143 AAATGTAAGACCATTTTTGACACTTG 57.353 30.769 0.00 0.00 41.11 3.16
2237 2377 6.767524 TGTAAGACCATTTTTGACACTTGT 57.232 33.333 0.00 0.00 0.00 3.16
2238 2378 6.559810 TGTAAGACCATTTTTGACACTTGTG 58.440 36.000 0.00 0.00 0.00 3.33
2239 2379 4.654091 AGACCATTTTTGACACTTGTGG 57.346 40.909 5.72 0.00 0.00 4.17
2240 2380 4.023291 AGACCATTTTTGACACTTGTGGT 58.977 39.130 5.72 0.00 40.89 4.16
2241 2381 4.359706 GACCATTTTTGACACTTGTGGTC 58.640 43.478 11.35 11.35 44.84 4.02
2242 2382 4.023291 ACCATTTTTGACACTTGTGGTCT 58.977 39.130 5.72 0.00 33.47 3.85
2243 2383 4.466015 ACCATTTTTGACACTTGTGGTCTT 59.534 37.500 5.72 0.00 33.47 3.01
2244 2384 5.654650 ACCATTTTTGACACTTGTGGTCTTA 59.345 36.000 5.72 0.00 33.47 2.10
2245 2385 5.977129 CCATTTTTGACACTTGTGGTCTTAC 59.023 40.000 5.72 0.00 36.26 2.34
2246 2386 6.405286 CCATTTTTGACACTTGTGGTCTTACA 60.405 38.462 5.72 0.00 36.26 2.41
2247 2387 6.767524 TTTTTGACACTTGTGGTCTTACAT 57.232 33.333 5.72 0.00 36.26 2.29
2248 2388 6.767524 TTTTGACACTTGTGGTCTTACATT 57.232 33.333 5.72 0.00 36.26 2.71
2249 2389 6.767524 TTTGACACTTGTGGTCTTACATTT 57.232 33.333 5.72 0.00 36.26 2.32
2250 2390 6.767524 TTGACACTTGTGGTCTTACATTTT 57.232 33.333 5.72 0.00 36.26 1.82
2251 2391 6.130298 TGACACTTGTGGTCTTACATTTTG 57.870 37.500 5.72 0.00 36.26 2.44
2252 2392 5.067153 TGACACTTGTGGTCTTACATTTTGG 59.933 40.000 5.72 0.00 36.26 3.28
2253 2393 4.953579 ACACTTGTGGTCTTACATTTTGGT 59.046 37.500 5.72 0.00 0.00 3.67
2254 2394 6.123651 ACACTTGTGGTCTTACATTTTGGTA 58.876 36.000 5.72 0.00 0.00 3.25
2255 2395 6.038936 ACACTTGTGGTCTTACATTTTGGTAC 59.961 38.462 5.72 0.00 0.00 3.34
2256 2396 5.237779 ACTTGTGGTCTTACATTTTGGTACG 59.762 40.000 0.00 0.00 0.00 3.67
2257 2397 4.066490 TGTGGTCTTACATTTTGGTACGG 58.934 43.478 0.00 0.00 0.00 4.02
2258 2398 4.202336 TGTGGTCTTACATTTTGGTACGGA 60.202 41.667 0.00 0.00 0.00 4.69
2259 2399 4.390909 GTGGTCTTACATTTTGGTACGGAG 59.609 45.833 0.00 0.00 0.00 4.63
2260 2400 3.937079 GGTCTTACATTTTGGTACGGAGG 59.063 47.826 0.00 0.00 0.00 4.30
2261 2401 3.937079 GTCTTACATTTTGGTACGGAGGG 59.063 47.826 0.00 0.00 0.00 4.30
2262 2402 3.839490 TCTTACATTTTGGTACGGAGGGA 59.161 43.478 0.00 0.00 0.00 4.20
2263 2403 2.781681 ACATTTTGGTACGGAGGGAG 57.218 50.000 0.00 0.00 0.00 4.30
2264 2404 1.982958 ACATTTTGGTACGGAGGGAGT 59.017 47.619 0.00 0.00 0.00 3.85
2265 2405 3.175594 ACATTTTGGTACGGAGGGAGTA 58.824 45.455 0.00 0.00 0.00 2.59
2266 2406 3.055602 ACATTTTGGTACGGAGGGAGTAC 60.056 47.826 0.00 0.00 42.58 2.73
2267 2407 2.610438 TTTGGTACGGAGGGAGTACT 57.390 50.000 0.00 0.00 42.81 2.73
2268 2408 2.610438 TTGGTACGGAGGGAGTACTT 57.390 50.000 0.00 0.00 42.81 2.24
2269 2409 2.134789 TGGTACGGAGGGAGTACTTC 57.865 55.000 0.00 0.00 42.81 3.01
2270 2410 1.355381 TGGTACGGAGGGAGTACTTCA 59.645 52.381 2.92 0.00 42.81 3.02
2271 2411 1.747924 GGTACGGAGGGAGTACTTCAC 59.252 57.143 2.92 0.00 42.81 3.18
2272 2412 2.440409 GTACGGAGGGAGTACTTCACA 58.560 52.381 2.92 0.00 40.75 3.58
2273 2413 2.005370 ACGGAGGGAGTACTTCACAA 57.995 50.000 2.92 0.00 0.00 3.33
2278 2418 3.166679 GAGGGAGTACTTCACAAGGAGT 58.833 50.000 2.92 0.00 0.00 3.85
2299 2439 0.249398 GGCAGACCTGATTACGTGGT 59.751 55.000 0.00 0.00 36.70 4.16
2320 2460 2.519013 AGTGGATTTGAACCCAGAAGC 58.481 47.619 0.00 0.00 32.28 3.86
2323 2463 1.200020 GGATTTGAACCCAGAAGCACG 59.800 52.381 0.00 0.00 0.00 5.34
2353 2493 6.311690 GTCCTCTTATCTCAGCTGTTTTGTAC 59.688 42.308 14.67 0.00 0.00 2.90
2392 2532 8.953665 ACCTGATAAGATGATTTTTATCCTCCT 58.046 33.333 7.64 0.00 36.10 3.69
2393 2533 9.228949 CCTGATAAGATGATTTTTATCCTCCTG 57.771 37.037 7.64 0.00 36.10 3.86
2411 2551 5.819901 CCTCCTGAGAACTAGCCTTTTAATG 59.180 44.000 0.00 0.00 0.00 1.90
2416 2556 4.335416 AGAACTAGCCTTTTAATGCAGCA 58.665 39.130 0.00 0.00 0.00 4.41
2420 2560 3.749665 AGCCTTTTAATGCAGCAAACA 57.250 38.095 0.00 0.00 0.00 2.83
2423 2563 3.747529 GCCTTTTAATGCAGCAAACATGT 59.252 39.130 0.00 0.00 0.00 3.21
2494 2635 2.287644 TGCACAAACACTTCATCTGACG 59.712 45.455 0.00 0.00 0.00 4.35
2495 2636 2.349817 GCACAAACACTTCATCTGACGG 60.350 50.000 0.00 0.00 0.00 4.79
2526 2667 6.804677 TGAGAACAATAAAAAGCTTTGCTCA 58.195 32.000 13.54 5.53 38.25 4.26
2535 2676 3.671008 AAGCTTTGCTCAATTGCATCA 57.329 38.095 0.00 0.00 42.96 3.07
2536 2677 3.887621 AGCTTTGCTCAATTGCATCAT 57.112 38.095 0.00 0.00 42.96 2.45
2547 2734 6.099159 TCAATTGCATCATGTCCTCAAAAA 57.901 33.333 0.00 0.00 0.00 1.94
2604 2792 2.057922 TCAAGGTGCTTCTCCTTCCTT 58.942 47.619 0.00 0.00 42.57 3.36
2605 2793 2.157738 CAAGGTGCTTCTCCTTCCTTG 58.842 52.381 7.66 7.66 45.47 3.61
2606 2794 0.037447 AGGTGCTTCTCCTTCCTTGC 59.963 55.000 0.00 0.00 30.18 4.01
2607 2795 0.250901 GGTGCTTCTCCTTCCTTGCA 60.251 55.000 0.00 0.00 0.00 4.08
2608 2796 1.615384 GGTGCTTCTCCTTCCTTGCAT 60.615 52.381 0.00 0.00 32.98 3.96
2651 2849 8.368668 CCCGTTCTATCTGGAATAATTTCTACT 58.631 37.037 0.00 0.00 32.16 2.57
2683 2900 5.824904 ATTCAGACATTGTATCACTTGGC 57.175 39.130 0.00 0.00 0.00 4.52
2687 2904 1.468520 ACATTGTATCACTTGGCGTGC 59.531 47.619 0.00 0.00 43.46 5.34
2700 2917 2.033194 GCGTGCCTAGGCGTTTCTT 61.033 57.895 28.28 0.00 45.51 2.52
2715 2932 4.503007 GCGTTTCTTTTTGGTTCCTTCTTC 59.497 41.667 0.00 0.00 0.00 2.87
2716 2933 5.678871 GCGTTTCTTTTTGGTTCCTTCTTCT 60.679 40.000 0.00 0.00 0.00 2.85
2717 2934 6.330278 CGTTTCTTTTTGGTTCCTTCTTCTT 58.670 36.000 0.00 0.00 0.00 2.52
2718 2935 7.477494 CGTTTCTTTTTGGTTCCTTCTTCTTA 58.523 34.615 0.00 0.00 0.00 2.10
2719 2936 8.135529 CGTTTCTTTTTGGTTCCTTCTTCTTAT 58.864 33.333 0.00 0.00 0.00 1.73
2720 2937 9.817809 GTTTCTTTTTGGTTCCTTCTTCTTATT 57.182 29.630 0.00 0.00 0.00 1.40
2760 2977 4.154195 TCTCAGAAAATTTAAGCGACAGCC 59.846 41.667 0.00 0.00 46.67 4.85
2794 3011 2.948315 GTCAATGCAGATTCTTCCCTCC 59.052 50.000 0.00 0.00 0.00 4.30
2795 3012 2.848694 TCAATGCAGATTCTTCCCTCCT 59.151 45.455 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 6.072286 ACAACTTCTATGAACCAAAGATGCAG 60.072 38.462 0.00 0.00 0.00 4.41
141 142 9.003112 CACACGCTATTATTTGAAAGAATGAAG 57.997 33.333 7.94 0.22 0.00 3.02
151 152 5.432645 TCAATCCCACACGCTATTATTTGA 58.567 37.500 0.00 0.00 0.00 2.69
152 153 5.749596 TCAATCCCACACGCTATTATTTG 57.250 39.130 0.00 0.00 0.00 2.32
153 154 6.735694 GCATTCAATCCCACACGCTATTATTT 60.736 38.462 0.00 0.00 0.00 1.40
162 163 1.452110 TCAGCATTCAATCCCACACG 58.548 50.000 0.00 0.00 0.00 4.49
191 193 9.683069 CAGCAAAATATTCATCAAAGGTATACC 57.317 33.333 14.54 14.54 0.00 2.73
194 196 8.416329 GGTCAGCAAAATATTCATCAAAGGTAT 58.584 33.333 0.00 0.00 0.00 2.73
196 198 6.438425 AGGTCAGCAAAATATTCATCAAAGGT 59.562 34.615 0.00 0.00 0.00 3.50
197 199 6.870769 AGGTCAGCAAAATATTCATCAAAGG 58.129 36.000 0.00 0.00 0.00 3.11
198 200 7.816031 ACAAGGTCAGCAAAATATTCATCAAAG 59.184 33.333 0.00 0.00 0.00 2.77
296 338 3.127376 TGCTGATGCATACACAACATCAC 59.873 43.478 0.00 0.87 43.85 3.06
361 403 3.701205 TCTTGCCACATTCAGCTTCTA 57.299 42.857 0.00 0.00 0.00 2.10
390 432 6.624352 TTTTCAGAACTCAAATCCACTGAG 57.376 37.500 0.00 0.00 44.90 3.35
429 471 3.088532 TGGGTGAAATTGCTACATCCAC 58.911 45.455 0.00 0.00 39.47 4.02
476 555 5.642165 TCTGTTCTACTCCCTCTGTAAACT 58.358 41.667 0.00 0.00 0.00 2.66
503 582 6.100569 TGGTACAATATACAGTGGGTTGCTAT 59.899 38.462 0.00 0.00 31.92 2.97
670 753 0.951558 AAACGCTCGTGCAATCCTTT 59.048 45.000 10.43 0.00 39.64 3.11
684 767 2.930040 TCGATTCTCCATCTTGAAACGC 59.070 45.455 0.00 0.00 38.01 4.84
723 809 0.109132 GGCGCAACCAATTGGAAGAG 60.109 55.000 31.22 22.20 38.86 2.85
751 837 1.504359 TACGTGTAAAGTGCAGCCAC 58.496 50.000 0.00 0.00 42.39 5.01
784 870 1.339055 TGTGTCTTAGCATGCCACCTC 60.339 52.381 15.66 3.44 0.00 3.85
893 986 5.755409 TGGAGTTTAAATAGTGCAGGAGA 57.245 39.130 0.00 0.00 0.00 3.71
929 1024 3.876914 TCTAAGCTGTGTTGTGTGGAAAG 59.123 43.478 0.00 0.00 0.00 2.62
1008 1110 0.622738 AGGAGAGTGCCATGGTGGAT 60.623 55.000 14.67 0.00 40.96 3.41
1059 1167 1.619654 CAAACACATTGGAGGAGGCA 58.380 50.000 0.00 0.00 35.27 4.75
1158 1269 0.818445 GGCCGAGATAGAGGACACGA 60.818 60.000 0.00 0.00 35.06 4.35
1290 1401 2.659063 CCGGCAGTGGATCACCTCA 61.659 63.158 0.00 0.00 34.49 3.86
1650 1761 2.125512 GAGAACATGGCGAGCCGT 60.126 61.111 9.78 6.29 39.42 5.68
1696 1807 3.728373 GGGACCCTTGCCGGTGAT 61.728 66.667 2.09 0.00 35.79 3.06
1710 1821 1.767692 GGCAAGGTTCTCAAGGGGA 59.232 57.895 0.00 0.00 0.00 4.81
1814 1925 0.323633 CATGCATCCCAAGTCCCACA 60.324 55.000 0.00 0.00 0.00 4.17
1815 1926 1.039233 CCATGCATCCCAAGTCCCAC 61.039 60.000 0.00 0.00 0.00 4.61
1830 1965 3.181467 ACACAACCCATGTTTGTTCCATG 60.181 43.478 7.11 0.00 41.46 3.66
2037 2177 1.528129 CTCTTGCAACCCTGAACTCC 58.472 55.000 0.00 0.00 0.00 3.85
2086 2226 6.258899 GCTCGTTTGTTTTCTTTCTTCTTCT 58.741 36.000 0.00 0.00 0.00 2.85
2087 2227 5.169738 CGCTCGTTTGTTTTCTTTCTTCTTC 59.830 40.000 0.00 0.00 0.00 2.87
2088 2228 5.028375 CGCTCGTTTGTTTTCTTTCTTCTT 58.972 37.500 0.00 0.00 0.00 2.52
2089 2229 4.094442 ACGCTCGTTTGTTTTCTTTCTTCT 59.906 37.500 0.00 0.00 0.00 2.85
2090 2230 4.202358 CACGCTCGTTTGTTTTCTTTCTTC 59.798 41.667 0.00 0.00 0.00 2.87
2091 2231 4.095610 CACGCTCGTTTGTTTTCTTTCTT 58.904 39.130 0.00 0.00 0.00 2.52
2092 2232 3.680789 CACGCTCGTTTGTTTTCTTTCT 58.319 40.909 0.00 0.00 0.00 2.52
2093 2233 2.213353 GCACGCTCGTTTGTTTTCTTTC 59.787 45.455 0.00 0.00 0.00 2.62
2110 2250 6.808212 ACTTGATTTTCCATTGAAATAGCACG 59.192 34.615 0.00 0.00 40.08 5.34
2155 2295 4.516698 ACTTAAACCATGAGCTCACTTGTG 59.483 41.667 20.97 13.41 0.00 3.33
2193 2333 1.171308 TTTGAGACGGAGGGAGTACG 58.829 55.000 0.00 0.00 0.00 3.67
2196 2336 1.978580 ACATTTTGAGACGGAGGGAGT 59.021 47.619 0.00 0.00 0.00 3.85
2197 2337 2.770164 ACATTTTGAGACGGAGGGAG 57.230 50.000 0.00 0.00 0.00 4.30
2222 2362 6.559810 TGTAAGACCACAAGTGTCAAAAATG 58.440 36.000 0.00 0.00 0.00 2.32
2225 2365 6.767524 AATGTAAGACCACAAGTGTCAAAA 57.232 33.333 0.00 0.00 30.84 2.44
2226 2366 6.767524 AAATGTAAGACCACAAGTGTCAAA 57.232 33.333 0.00 0.00 30.84 2.69
2227 2367 6.405286 CCAAAATGTAAGACCACAAGTGTCAA 60.405 38.462 0.00 0.00 30.84 3.18
2228 2368 5.067153 CCAAAATGTAAGACCACAAGTGTCA 59.933 40.000 0.00 0.00 30.84 3.58
2229 2369 5.067283 ACCAAAATGTAAGACCACAAGTGTC 59.933 40.000 0.00 0.00 30.84 3.67
2230 2370 4.953579 ACCAAAATGTAAGACCACAAGTGT 59.046 37.500 0.00 0.00 30.84 3.55
2231 2371 5.514274 ACCAAAATGTAAGACCACAAGTG 57.486 39.130 0.00 0.00 30.84 3.16
2232 2372 5.237779 CGTACCAAAATGTAAGACCACAAGT 59.762 40.000 0.00 0.00 30.84 3.16
2233 2373 5.334569 CCGTACCAAAATGTAAGACCACAAG 60.335 44.000 0.00 0.00 30.84 3.16
2234 2374 4.515944 CCGTACCAAAATGTAAGACCACAA 59.484 41.667 0.00 0.00 30.84 3.33
2235 2375 4.066490 CCGTACCAAAATGTAAGACCACA 58.934 43.478 0.00 0.00 0.00 4.17
2236 2376 4.317488 TCCGTACCAAAATGTAAGACCAC 58.683 43.478 0.00 0.00 0.00 4.16
2237 2377 4.563993 CCTCCGTACCAAAATGTAAGACCA 60.564 45.833 0.00 0.00 0.00 4.02
2238 2378 3.937079 CCTCCGTACCAAAATGTAAGACC 59.063 47.826 0.00 0.00 0.00 3.85
2239 2379 3.937079 CCCTCCGTACCAAAATGTAAGAC 59.063 47.826 0.00 0.00 0.00 3.01
2240 2380 3.839490 TCCCTCCGTACCAAAATGTAAGA 59.161 43.478 0.00 0.00 0.00 2.10
2241 2381 4.189231 CTCCCTCCGTACCAAAATGTAAG 58.811 47.826 0.00 0.00 0.00 2.34
2242 2382 3.583966 ACTCCCTCCGTACCAAAATGTAA 59.416 43.478 0.00 0.00 0.00 2.41
2243 2383 3.175594 ACTCCCTCCGTACCAAAATGTA 58.824 45.455 0.00 0.00 0.00 2.29
2244 2384 1.982958 ACTCCCTCCGTACCAAAATGT 59.017 47.619 0.00 0.00 0.00 2.71
2245 2385 2.781681 ACTCCCTCCGTACCAAAATG 57.218 50.000 0.00 0.00 0.00 2.32
2246 2386 3.447950 AGTACTCCCTCCGTACCAAAAT 58.552 45.455 0.00 0.00 38.34 1.82
2247 2387 2.893424 AGTACTCCCTCCGTACCAAAA 58.107 47.619 0.00 0.00 38.34 2.44
2248 2388 2.610438 AGTACTCCCTCCGTACCAAA 57.390 50.000 0.00 0.00 38.34 3.28
2249 2389 2.225091 TGAAGTACTCCCTCCGTACCAA 60.225 50.000 0.00 0.00 38.34 3.67
2250 2390 1.355381 TGAAGTACTCCCTCCGTACCA 59.645 52.381 0.00 0.00 38.34 3.25
2251 2391 1.747924 GTGAAGTACTCCCTCCGTACC 59.252 57.143 0.00 0.00 38.34 3.34
2252 2392 2.440409 TGTGAAGTACTCCCTCCGTAC 58.560 52.381 0.00 0.00 37.96 3.67
2253 2393 2.885135 TGTGAAGTACTCCCTCCGTA 57.115 50.000 0.00 0.00 0.00 4.02
2254 2394 1.893801 CTTGTGAAGTACTCCCTCCGT 59.106 52.381 0.00 0.00 0.00 4.69
2255 2395 1.204941 CCTTGTGAAGTACTCCCTCCG 59.795 57.143 0.00 0.00 0.00 4.63
2256 2396 2.498078 CTCCTTGTGAAGTACTCCCTCC 59.502 54.545 0.00 0.00 0.00 4.30
2257 2397 3.166679 ACTCCTTGTGAAGTACTCCCTC 58.833 50.000 0.00 0.00 0.00 4.30
2258 2398 3.261818 ACTCCTTGTGAAGTACTCCCT 57.738 47.619 0.00 0.00 0.00 4.20
2259 2399 3.447944 CCTACTCCTTGTGAAGTACTCCC 59.552 52.174 0.00 0.00 0.00 4.30
2260 2400 3.119065 GCCTACTCCTTGTGAAGTACTCC 60.119 52.174 0.00 0.00 0.00 3.85
2261 2401 3.510360 TGCCTACTCCTTGTGAAGTACTC 59.490 47.826 0.00 0.00 0.00 2.59
2262 2402 3.507411 TGCCTACTCCTTGTGAAGTACT 58.493 45.455 0.00 0.00 0.00 2.73
2263 2403 3.510360 TCTGCCTACTCCTTGTGAAGTAC 59.490 47.826 0.00 0.00 0.00 2.73
2264 2404 3.510360 GTCTGCCTACTCCTTGTGAAGTA 59.490 47.826 0.00 0.00 0.00 2.24
2265 2405 2.300437 GTCTGCCTACTCCTTGTGAAGT 59.700 50.000 0.00 0.00 0.00 3.01
2266 2406 2.354203 GGTCTGCCTACTCCTTGTGAAG 60.354 54.545 0.00 0.00 0.00 3.02
2267 2407 1.623811 GGTCTGCCTACTCCTTGTGAA 59.376 52.381 0.00 0.00 0.00 3.18
2268 2408 1.203187 AGGTCTGCCTACTCCTTGTGA 60.203 52.381 0.00 0.00 44.90 3.58
2269 2409 1.066573 CAGGTCTGCCTACTCCTTGTG 60.067 57.143 0.00 0.00 44.97 3.33
2270 2410 1.203187 TCAGGTCTGCCTACTCCTTGT 60.203 52.381 0.00 0.00 44.97 3.16
2271 2411 1.561643 TCAGGTCTGCCTACTCCTTG 58.438 55.000 0.00 0.00 44.97 3.61
2272 2412 2.559381 ATCAGGTCTGCCTACTCCTT 57.441 50.000 0.00 0.00 44.97 3.36
2273 2413 2.559381 AATCAGGTCTGCCTACTCCT 57.441 50.000 0.00 0.00 44.97 3.69
2278 2418 1.754803 CCACGTAATCAGGTCTGCCTA 59.245 52.381 0.00 0.00 44.97 3.93
2299 2439 3.073798 TGCTTCTGGGTTCAAATCCACTA 59.926 43.478 0.00 0.00 33.26 2.74
2320 2460 2.685388 TGAGATAAGAGGACAGCTCGTG 59.315 50.000 0.00 0.00 0.00 4.35
2323 2463 3.369546 GCTGAGATAAGAGGACAGCTC 57.630 52.381 0.00 0.00 46.66 4.09
2367 2507 9.228949 CAGGAGGATAAAAATCATCTTATCAGG 57.771 37.037 0.75 0.00 36.60 3.86
2379 2519 6.388394 AGGCTAGTTCTCAGGAGGATAAAAAT 59.612 38.462 0.00 0.00 0.00 1.82
2381 2521 5.281314 AGGCTAGTTCTCAGGAGGATAAAA 58.719 41.667 0.00 0.00 0.00 1.52
2382 2522 4.884961 AGGCTAGTTCTCAGGAGGATAAA 58.115 43.478 0.00 0.00 0.00 1.40
2384 2524 4.544564 AAGGCTAGTTCTCAGGAGGATA 57.455 45.455 0.00 0.00 0.00 2.59
2385 2525 3.413105 AAGGCTAGTTCTCAGGAGGAT 57.587 47.619 0.00 0.00 0.00 3.24
2388 2528 5.295540 GCATTAAAAGGCTAGTTCTCAGGAG 59.704 44.000 0.00 0.00 32.08 3.69
2390 2530 4.943705 TGCATTAAAAGGCTAGTTCTCAGG 59.056 41.667 0.77 0.00 36.52 3.86
2391 2531 5.448360 GCTGCATTAAAAGGCTAGTTCTCAG 60.448 44.000 0.77 0.00 36.52 3.35
2392 2532 4.396166 GCTGCATTAAAAGGCTAGTTCTCA 59.604 41.667 0.77 0.00 36.52 3.27
2393 2533 4.396166 TGCTGCATTAAAAGGCTAGTTCTC 59.604 41.667 0.00 0.00 36.52 2.87
2394 2534 4.335416 TGCTGCATTAAAAGGCTAGTTCT 58.665 39.130 0.00 0.00 36.52 3.01
2411 2551 3.631145 TTTCTGAGACATGTTTGCTGC 57.369 42.857 0.00 0.00 0.00 5.25
2416 2556 7.396540 AACTGAAGTTTTCTGAGACATGTTT 57.603 32.000 0.00 0.00 33.93 2.83
2420 2560 6.712095 TGCATAACTGAAGTTTTCTGAGACAT 59.288 34.615 0.21 0.00 39.31 3.06
2423 2563 9.102757 GATATGCATAACTGAAGTTTTCTGAGA 57.897 33.333 11.13 0.00 39.31 3.27
2463 2603 3.550820 AGTGTTTGTGCAGGTCATTGTA 58.449 40.909 0.00 0.00 0.00 2.41
2471 2611 2.880268 TCAGATGAAGTGTTTGTGCAGG 59.120 45.455 0.00 0.00 0.00 4.85
2494 2635 8.100508 AGCTTTTTATTGTTCTCAGTACTTCC 57.899 34.615 0.00 0.00 0.00 3.46
2495 2636 9.952188 AAAGCTTTTTATTGTTCTCAGTACTTC 57.048 29.630 5.69 0.00 0.00 3.01
2499 2640 7.940850 AGCAAAGCTTTTTATTGTTCTCAGTA 58.059 30.769 9.53 0.00 33.89 2.74
2569 2756 7.651027 AGCACCTTGATAGCTTGATTTATTT 57.349 32.000 0.00 0.00 34.37 1.40
2570 2757 7.651027 AAGCACCTTGATAGCTTGATTTATT 57.349 32.000 0.00 0.00 45.99 1.40
2583 2771 2.273619 AGGAAGGAGAAGCACCTTGAT 58.726 47.619 0.00 0.00 46.14 2.57
2605 2793 3.137533 GGAGGAAGAACATGCTAGATGC 58.862 50.000 0.00 0.00 43.25 3.91
2606 2794 3.737850 GGGAGGAAGAACATGCTAGATG 58.262 50.000 0.00 0.00 0.00 2.90
2607 2795 2.366916 CGGGAGGAAGAACATGCTAGAT 59.633 50.000 0.00 0.00 0.00 1.98
2608 2796 1.757118 CGGGAGGAAGAACATGCTAGA 59.243 52.381 0.00 0.00 0.00 2.43
2624 2822 7.374975 AGAAATTATTCCAGATAGAACGGGA 57.625 36.000 0.00 0.00 36.12 5.14
2651 2849 3.264193 ACAATGTCTGAATAGCAGGGACA 59.736 43.478 0.00 0.00 44.98 4.02
2683 2900 0.872388 AAAAGAAACGCCTAGGCACG 59.128 50.000 32.47 19.84 42.06 5.34
2687 2904 3.305131 GGAACCAAAAAGAAACGCCTAGG 60.305 47.826 3.67 3.67 0.00 3.02
2737 2954 4.154195 GGCTGTCGCTTAAATTTTCTGAGA 59.846 41.667 0.00 0.00 36.09 3.27
2738 2955 4.083324 TGGCTGTCGCTTAAATTTTCTGAG 60.083 41.667 0.00 0.00 36.09 3.35
2751 2968 0.679505 TGAAACTAGTGGCTGTCGCT 59.320 50.000 0.00 0.00 39.84 4.93
2760 2977 6.304356 TCTGCATTGACTTTGAAACTAGTG 57.696 37.500 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.