Multiple sequence alignment - TraesCS5B01G392700

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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 TraesCS5B01G392700 chr5B 100.000 2553 0 0 1 2553 571320647 571323199 0.000000e+00 4715.0
1 TraesCS5B01G392700 chr5A 91.675 2126 142 21 1 2115 584662298 584664399 0.000000e+00 2913.0
2 TraesCS5B01G392700 chr5A 87.956 274 13 10 2120 2374 584664485 584664757 3.190000e-79 305.0
3 TraesCS5B01G392700 chr5D 91.186 1838 79 31 613 2374 464225959 464227789 0.000000e+00 2420.0
4 TraesCS5B01G392700 chr5D 90.193 622 52 8 2 621 464224949 464225563 0.000000e+00 802.0
5 TraesCS5B01G392700 chr5D 87.402 127 12 2 2373 2497 286926479 286926603 2.650000e-30 143.0
6 TraesCS5B01G392700 chr5D 86.992 123 16 0 2375 2497 265122875 265122997 3.430000e-29 139.0
7 TraesCS5B01G392700 chr5D 95.238 63 2 1 2487 2549 176623071 176623132 5.810000e-17 99.0
8 TraesCS5B01G392700 chr6B 89.431 123 13 0 2375 2497 315995953 315995831 3.400000e-34 156.0
9 TraesCS5B01G392700 chr6B 98.276 58 1 0 2492 2549 335808148 335808205 4.490000e-18 102.0
10 TraesCS5B01G392700 chr2D 87.603 121 15 0 2372 2492 262913701 262913821 9.520000e-30 141.0
11 TraesCS5B01G392700 chr2D 86.555 119 16 0 2374 2492 385143748 385143630 5.730000e-27 132.0
12 TraesCS5B01G392700 chr2D 86.290 124 12 5 2375 2496 331915327 331915447 2.060000e-26 130.0
13 TraesCS5B01G392700 chr1B 86.400 125 16 1 2373 2497 168298332 168298209 4.430000e-28 135.0
14 TraesCS5B01G392700 chr4A 86.777 121 14 2 2373 2492 146189087 146189206 1.590000e-27 134.0
15 TraesCS5B01G392700 chr4A 93.846 65 3 1 2487 2551 395539359 395539296 2.090000e-16 97.1
16 TraesCS5B01G392700 chr7D 86.555 119 16 0 2374 2492 626413886 626414004 5.730000e-27 132.0
17 TraesCS5B01G392700 chr7D 95.238 63 2 1 2487 2549 177496078 177496139 5.810000e-17 99.0
18 TraesCS5B01G392700 chr2B 98.333 60 1 0 2494 2553 161082998 161083057 3.470000e-19 106.0
19 TraesCS5B01G392700 chr2B 90.909 77 5 2 2477 2553 331739981 331740055 4.490000e-18 102.0
20 TraesCS5B01G392700 chr7B 98.276 58 1 0 2492 2549 189775635 189775692 4.490000e-18 102.0
21 TraesCS5B01G392700 chr4B 95.238 63 2 1 2487 2549 230944349 230944288 5.810000e-17 99.0
22 TraesCS5B01G392700 chr4D 85.714 91 9 4 2463 2552 201365593 201365506 2.700000e-15 93.5


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 TraesCS5B01G392700 chr5B 571320647 571323199 2552 False 4715 4715 100.0000 1 2553 1 chr5B.!!$F1 2552
1 TraesCS5B01G392700 chr5A 584662298 584664757 2459 False 1609 2913 89.8155 1 2374 2 chr5A.!!$F1 2373
2 TraesCS5B01G392700 chr5D 464224949 464227789 2840 False 1611 2420 90.6895 2 2374 2 chr5D.!!$F4 2372

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
788 1197 0.040514 CGTGCACGAAATGAGGCAAA 60.041 50.0 34.93 0.0 43.02 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2957 0.036875 AAGCAGGCAAGTCTGGGTAC 59.963 55.0 3.62 0.0 35.43 3.34 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
119 121 1.075601 TCAACCCCATCCTTTGCTCT 58.924 50.000 0.00 0.00 0.00 4.09
122 124 1.972588 ACCCCATCCTTTGCTCTAGT 58.027 50.000 0.00 0.00 0.00 2.57
162 164 1.001406 CTCAACAGAAACTCGCCTCCT 59.999 52.381 0.00 0.00 0.00 3.69
172 174 1.355066 CTCGCCTCCTTTTCAGTCGC 61.355 60.000 0.00 0.00 0.00 5.19
174 176 0.108804 CGCCTCCTTTTCAGTCGCTA 60.109 55.000 0.00 0.00 0.00 4.26
272 274 4.640771 ACACTTAAGGTCCATGTGTCAT 57.359 40.909 7.53 0.00 37.29 3.06
278 280 1.304282 GTCCATGTGTCATGGGGCT 59.696 57.895 23.07 0.00 39.60 5.19
295 297 1.704007 GCTAGGATCAAGCAGGGCCT 61.704 60.000 0.00 0.00 39.83 5.19
324 327 5.615289 CCATAGGGGAGAAATACAACTCAG 58.385 45.833 0.00 0.00 40.01 3.35
345 348 4.647399 CAGGGGTAAAAGAAAAGTCAACCA 59.353 41.667 0.00 0.00 0.00 3.67
350 353 7.147863 GGGGTAAAAGAAAAGTCAACCAAAGTA 60.148 37.037 0.00 0.00 0.00 2.24
355 358 5.891451 AGAAAAGTCAACCAAAGTAACTGC 58.109 37.500 0.00 0.00 0.00 4.40
356 359 4.649088 AAAGTCAACCAAAGTAACTGCC 57.351 40.909 0.00 0.00 0.00 4.85
407 410 3.132824 GCTGAAATCACCTAAATTGGGGG 59.867 47.826 0.00 0.00 0.00 5.40
450 453 4.582656 TCAACCACACATAAACTTGAAGGG 59.417 41.667 0.00 0.00 0.00 3.95
462 465 6.699575 AAACTTGAAGGGGATATCGAATTG 57.300 37.500 0.00 0.00 0.00 2.32
482 485 2.006888 GTCACATTGACGGGTATGGTG 58.993 52.381 0.00 0.00 37.67 4.17
489 492 2.538222 TGACGGGTATGGTGAGGTTAA 58.462 47.619 0.00 0.00 0.00 2.01
548 551 6.658831 ACACACAATTCTACGTGAATGAAAG 58.341 36.000 12.06 7.23 43.99 2.62
574 577 7.376335 ACTAAGGAAAAAGTACCAACTCTCT 57.624 36.000 0.00 0.00 33.75 3.10
585 588 1.134965 CCAACTCTCTTGCCCGAGTAG 60.135 57.143 0.00 0.37 39.44 2.57
607 610 0.313672 AATCACGCGGTGCAAATTGT 59.686 45.000 12.47 0.00 32.98 2.71
611 614 1.135831 CACGCGGTGCAAATTGTGATA 60.136 47.619 12.47 0.00 0.00 2.15
626 1033 5.339008 TTGTGATATACTCTTCAAGGCGT 57.661 39.130 0.00 0.00 0.00 5.68
637 1044 1.445410 CAAGGCGTGATCGAACCGA 60.445 57.895 0.00 0.00 41.13 4.69
720 1127 1.255882 TGCGTGGCATGAATCCTTTT 58.744 45.000 11.71 0.00 31.71 2.27
788 1197 0.040514 CGTGCACGAAATGAGGCAAA 60.041 50.000 34.93 0.00 43.02 3.68
805 1214 7.504403 TGAGGCAAAAATTAATTTCTCCACAA 58.496 30.769 13.68 0.00 0.00 3.33
888 1305 5.334414 GGAAGATTAGAGCAATTACATGGCG 60.334 44.000 0.00 0.00 0.00 5.69
951 1369 1.676014 GCTAAAAGCTTCGAGGAGCCA 60.676 52.381 0.00 0.00 43.74 4.75
1013 1431 1.956477 CCAAGAGGACCCAACACAAAG 59.044 52.381 0.00 0.00 36.89 2.77
1217 1641 2.518112 TGCCTGCACGCCTTCAAA 60.518 55.556 5.19 0.00 0.00 2.69
1229 1653 1.677217 GCCTTCAAAGAGTCCTGCGAT 60.677 52.381 0.00 0.00 0.00 4.58
1304 1728 4.980805 GCCACAACCCTCGACGCA 62.981 66.667 0.00 0.00 0.00 5.24
1308 1732 2.201022 ACAACCCTCGACGCACTCT 61.201 57.895 0.00 0.00 0.00 3.24
1393 1820 4.883354 GCAGGATGGGAAGGGCCG 62.883 72.222 0.00 0.00 37.63 6.13
1447 1874 2.027751 GGCCGACGATGTCTAGCC 59.972 66.667 10.73 10.73 40.50 3.93
1462 1896 0.105709 TAGCCCGATCCATCTGGTCA 60.106 55.000 0.00 0.00 34.13 4.02
1471 1905 0.037303 CCATCTGGTCACTTGTGGCT 59.963 55.000 5.33 0.00 0.00 4.75
1562 1997 8.619146 AATGTTGTAATGCAGATAAATTCGTG 57.381 30.769 0.00 0.00 0.00 4.35
1705 2141 1.720781 AAACAGGGGTACGTACAGGT 58.279 50.000 26.02 14.80 0.00 4.00
1706 2142 1.720781 AACAGGGGTACGTACAGGTT 58.279 50.000 26.02 19.07 0.00 3.50
1707 2143 2.603075 ACAGGGGTACGTACAGGTTA 57.397 50.000 26.02 0.00 0.00 2.85
1708 2144 2.888212 ACAGGGGTACGTACAGGTTAA 58.112 47.619 26.02 0.00 0.00 2.01
1733 2169 0.040958 GGAGTTGCAAGTTGCTGTCG 60.041 55.000 27.17 0.00 45.31 4.35
1805 2241 6.109156 TCCACATACAAGAGTAAGAAGCAA 57.891 37.500 0.00 0.00 33.13 3.91
1880 2330 3.032459 CCAAAGTAGGAGTAGGACCCTC 58.968 54.545 0.00 0.00 34.11 4.30
1972 2425 1.881973 CAAATATCCTGTGGCCATCCG 59.118 52.381 9.72 0.00 34.14 4.18
2009 2462 6.317893 ACACGATTCAGTTTAGGAAGTTTGTT 59.682 34.615 0.00 0.00 0.00 2.83
2115 2568 0.604780 ACTGCAGTGTCATGTCAGCC 60.605 55.000 20.97 0.00 31.59 4.85
2143 2677 1.686110 AAGGAGACCGGTAGGCCTG 60.686 63.158 17.99 0.00 42.76 4.85
2196 2734 1.301677 GAAGGCAAGGCTCTCCGTTG 61.302 60.000 0.00 0.00 37.47 4.10
2219 2773 1.078143 GATGGTCCGAGGCAAAGCT 60.078 57.895 0.00 0.00 0.00 3.74
2221 2775 0.678048 ATGGTCCGAGGCAAAGCTTC 60.678 55.000 0.00 0.00 0.00 3.86
2232 2787 3.385755 AGGCAAAGCTTCTTTTGTCATGT 59.614 39.130 0.00 0.00 43.34 3.21
2243 2798 4.988540 TCTTTTGTCATGTACTCCAGTTCG 59.011 41.667 0.00 0.00 0.00 3.95
2255 2810 1.148310 CCAGTTCGATCGCACAACTT 58.852 50.000 19.74 0.00 0.00 2.66
2333 2893 2.751166 TTGACACTGCTAGCTTCTCC 57.249 50.000 17.23 3.32 0.00 3.71
2341 2901 1.137086 TGCTAGCTTCTCCATTCGACC 59.863 52.381 17.23 0.00 0.00 4.79
2345 2905 0.458669 GCTTCTCCATTCGACCGGTA 59.541 55.000 7.34 0.00 0.00 4.02
2365 2926 9.675464 ACCGGTAGATAAAATTATGTCTTTTCA 57.325 29.630 4.49 0.00 0.00 2.69
2378 2939 6.712241 ATGTCTTTTCATCTAACACTGTCG 57.288 37.500 0.00 0.00 0.00 4.35
2379 2940 4.988540 TGTCTTTTCATCTAACACTGTCGG 59.011 41.667 0.00 0.00 0.00 4.79
2380 2941 3.994392 TCTTTTCATCTAACACTGTCGGC 59.006 43.478 0.00 0.00 0.00 5.54
2381 2942 3.394674 TTTCATCTAACACTGTCGGCA 57.605 42.857 0.00 0.00 0.00 5.69
2382 2943 3.610040 TTCATCTAACACTGTCGGCAT 57.390 42.857 0.00 0.00 0.00 4.40
2383 2944 3.610040 TCATCTAACACTGTCGGCATT 57.390 42.857 0.00 0.00 0.00 3.56
2384 2945 3.521560 TCATCTAACACTGTCGGCATTC 58.478 45.455 0.00 0.00 0.00 2.67
2385 2946 3.195610 TCATCTAACACTGTCGGCATTCT 59.804 43.478 0.00 0.00 0.00 2.40
2386 2947 2.959516 TCTAACACTGTCGGCATTCTG 58.040 47.619 0.00 0.00 0.00 3.02
2387 2948 1.394917 CTAACACTGTCGGCATTCTGC 59.605 52.381 0.00 0.00 44.08 4.26
2388 2949 1.568612 AACACTGTCGGCATTCTGCG 61.569 55.000 0.00 0.00 46.21 5.18
2389 2950 1.737735 CACTGTCGGCATTCTGCGA 60.738 57.895 0.00 0.00 46.21 5.10
2390 2951 1.005037 ACTGTCGGCATTCTGCGAA 60.005 52.632 0.00 0.00 46.21 4.70
2391 2952 1.291877 ACTGTCGGCATTCTGCGAAC 61.292 55.000 0.00 0.00 46.21 3.95
2392 2953 1.970917 CTGTCGGCATTCTGCGAACC 61.971 60.000 0.00 0.00 46.21 3.62
2393 2954 2.032634 GTCGGCATTCTGCGAACCA 61.033 57.895 0.00 0.00 46.21 3.67
2394 2955 1.741401 TCGGCATTCTGCGAACCAG 60.741 57.895 0.00 0.00 46.21 4.00
2395 2956 2.753966 CGGCATTCTGCGAACCAGG 61.754 63.158 0.00 0.00 46.21 4.45
2396 2957 2.409870 GGCATTCTGCGAACCAGGG 61.410 63.158 0.00 0.00 46.21 4.45
2397 2958 1.675641 GCATTCTGCGAACCAGGGT 60.676 57.895 0.00 0.00 42.05 4.34
2398 2959 0.392461 GCATTCTGCGAACCAGGGTA 60.392 55.000 0.00 0.00 42.05 3.69
2399 2960 1.369625 CATTCTGCGAACCAGGGTAC 58.630 55.000 0.00 0.00 42.05 3.34
2413 2974 1.377333 GGTACCCAGACTTGCCTGC 60.377 63.158 0.00 0.00 32.97 4.85
2414 2975 1.679898 GTACCCAGACTTGCCTGCT 59.320 57.895 0.00 0.00 32.97 4.24
2415 2976 0.036875 GTACCCAGACTTGCCTGCTT 59.963 55.000 0.00 0.00 32.97 3.91
2416 2977 1.278127 GTACCCAGACTTGCCTGCTTA 59.722 52.381 0.00 0.00 32.97 3.09
2417 2978 0.036875 ACCCAGACTTGCCTGCTTAC 59.963 55.000 0.00 0.00 32.97 2.34
2418 2979 1.021390 CCCAGACTTGCCTGCTTACG 61.021 60.000 0.00 0.00 32.97 3.18
2419 2980 1.021390 CCAGACTTGCCTGCTTACGG 61.021 60.000 0.00 0.00 32.97 4.02
2420 2981 0.320771 CAGACTTGCCTGCTTACGGT 60.321 55.000 0.00 0.00 0.00 4.83
2421 2982 0.037232 AGACTTGCCTGCTTACGGTC 60.037 55.000 0.00 0.00 0.00 4.79
2422 2983 1.003718 ACTTGCCTGCTTACGGTCC 60.004 57.895 0.00 0.00 0.00 4.46
2423 2984 1.003839 CTTGCCTGCTTACGGTCCA 60.004 57.895 0.00 0.00 0.00 4.02
2424 2985 0.392998 CTTGCCTGCTTACGGTCCAT 60.393 55.000 0.00 0.00 0.00 3.41
2425 2986 0.676466 TTGCCTGCTTACGGTCCATG 60.676 55.000 0.00 0.00 0.00 3.66
2426 2987 1.819632 GCCTGCTTACGGTCCATGG 60.820 63.158 4.97 4.97 0.00 3.66
2427 2988 1.819632 CCTGCTTACGGTCCATGGC 60.820 63.158 6.96 1.78 0.00 4.40
2428 2989 2.125310 TGCTTACGGTCCATGGCG 60.125 61.111 6.96 8.69 0.00 5.69
2429 2990 2.125269 GCTTACGGTCCATGGCGT 60.125 61.111 19.27 19.27 0.00 5.68
2430 2991 2.461110 GCTTACGGTCCATGGCGTG 61.461 63.158 22.85 11.35 0.00 5.34
2438 2999 2.903855 CCATGGCGTGGCTCCATC 60.904 66.667 13.80 0.00 42.11 3.51
2439 3000 3.274586 CATGGCGTGGCTCCATCG 61.275 66.667 0.00 0.00 42.11 3.84
2440 3001 3.469970 ATGGCGTGGCTCCATCGA 61.470 61.111 12.62 0.00 40.08 3.59
2441 3002 3.740128 ATGGCGTGGCTCCATCGAC 62.740 63.158 12.62 10.82 40.08 4.20
2447 3008 4.899239 GGCTCCATCGACGGCCTG 62.899 72.222 0.00 0.00 41.20 4.85
2448 3009 3.838271 GCTCCATCGACGGCCTGA 61.838 66.667 0.00 0.00 0.00 3.86
2449 3010 3.133014 CTCCATCGACGGCCTGAT 58.867 61.111 0.00 0.00 0.00 2.90
2450 3011 1.806461 GCTCCATCGACGGCCTGATA 61.806 60.000 0.00 0.00 0.00 2.15
2451 3012 0.039074 CTCCATCGACGGCCTGATAC 60.039 60.000 0.00 0.00 0.00 2.24
2452 3013 1.371758 CCATCGACGGCCTGATACG 60.372 63.158 0.00 0.00 0.00 3.06
2453 3014 1.371758 CATCGACGGCCTGATACGG 60.372 63.158 0.00 0.00 0.00 4.02
2460 3021 3.151906 GCCTGATACGGCCCATCT 58.848 61.111 12.08 0.00 44.41 2.90
2461 3022 1.004440 GCCTGATACGGCCCATCTC 60.004 63.158 12.08 0.00 44.41 2.75
2462 3023 1.674057 CCTGATACGGCCCATCTCC 59.326 63.158 12.08 0.00 0.00 3.71
2463 3024 1.121407 CCTGATACGGCCCATCTCCA 61.121 60.000 12.08 0.00 0.00 3.86
2464 3025 0.758734 CTGATACGGCCCATCTCCAA 59.241 55.000 12.08 0.00 0.00 3.53
2465 3026 0.468226 TGATACGGCCCATCTCCAAC 59.532 55.000 12.08 0.00 0.00 3.77
2466 3027 0.250338 GATACGGCCCATCTCCAACC 60.250 60.000 0.00 0.00 0.00 3.77
2467 3028 0.986019 ATACGGCCCATCTCCAACCA 60.986 55.000 0.00 0.00 0.00 3.67
2468 3029 1.622607 TACGGCCCATCTCCAACCAG 61.623 60.000 0.00 0.00 0.00 4.00
2469 3030 2.276740 GGCCCATCTCCAACCAGG 59.723 66.667 0.00 0.00 39.47 4.45
2470 3031 2.308722 GGCCCATCTCCAACCAGGA 61.309 63.158 0.00 0.00 46.75 3.86
2471 3032 1.077429 GCCCATCTCCAACCAGGAC 60.077 63.158 0.00 0.00 43.07 3.85
2472 3033 1.852157 GCCCATCTCCAACCAGGACA 61.852 60.000 0.00 0.00 43.07 4.02
2473 3034 0.698238 CCCATCTCCAACCAGGACAA 59.302 55.000 0.00 0.00 43.07 3.18
2474 3035 1.340405 CCCATCTCCAACCAGGACAAG 60.340 57.143 0.00 0.00 43.07 3.16
2475 3036 1.340405 CCATCTCCAACCAGGACAAGG 60.340 57.143 0.00 0.00 43.07 3.61
2476 3037 0.329596 ATCTCCAACCAGGACAAGGC 59.670 55.000 0.00 0.00 43.07 4.35
2477 3038 1.059584 TCTCCAACCAGGACAAGGCA 61.060 55.000 0.00 0.00 43.07 4.75
2478 3039 0.178992 CTCCAACCAGGACAAGGCAA 60.179 55.000 0.00 0.00 43.07 4.52
2479 3040 0.178992 TCCAACCAGGACAAGGCAAG 60.179 55.000 0.00 0.00 43.07 4.01
2480 3041 0.178992 CCAACCAGGACAAGGCAAGA 60.179 55.000 0.00 0.00 41.22 3.02
2481 3042 0.954452 CAACCAGGACAAGGCAAGAC 59.046 55.000 0.00 0.00 0.00 3.01
2482 3043 0.178990 AACCAGGACAAGGCAAGACC 60.179 55.000 0.00 0.00 39.61 3.85
2483 3044 1.303643 CCAGGACAAGGCAAGACCC 60.304 63.158 0.00 0.00 40.58 4.46
2484 3045 1.763770 CAGGACAAGGCAAGACCCT 59.236 57.895 0.00 0.00 40.58 4.34
2485 3046 0.322008 CAGGACAAGGCAAGACCCTC 60.322 60.000 0.00 0.00 40.58 4.30
2486 3047 1.376037 GGACAAGGCAAGACCCTCG 60.376 63.158 0.00 0.00 40.58 4.63
2487 3048 2.032681 ACAAGGCAAGACCCTCGC 59.967 61.111 0.00 0.00 40.58 5.03
2488 3049 3.121030 CAAGGCAAGACCCTCGCG 61.121 66.667 0.00 0.00 40.58 5.87
2489 3050 3.311110 AAGGCAAGACCCTCGCGA 61.311 61.111 9.26 9.26 40.58 5.87
2490 3051 3.302347 AAGGCAAGACCCTCGCGAG 62.302 63.158 29.06 29.06 40.58 5.03
2520 3081 3.435186 GCAGAGCGGCAGGTTTCC 61.435 66.667 1.45 0.00 0.00 3.13
2521 3082 2.348998 CAGAGCGGCAGGTTTCCT 59.651 61.111 1.45 0.00 0.00 3.36
2522 3083 1.743252 CAGAGCGGCAGGTTTCCTC 60.743 63.158 1.45 0.00 0.00 3.71
2523 3084 1.915769 AGAGCGGCAGGTTTCCTCT 60.916 57.895 1.45 0.00 0.00 3.69
2524 3085 1.003233 GAGCGGCAGGTTTCCTCTT 60.003 57.895 1.45 0.00 0.00 2.85
2525 3086 0.606673 GAGCGGCAGGTTTCCTCTTT 60.607 55.000 1.45 0.00 0.00 2.52
2526 3087 0.890996 AGCGGCAGGTTTCCTCTTTG 60.891 55.000 1.45 0.00 0.00 2.77
2527 3088 1.866853 GCGGCAGGTTTCCTCTTTGG 61.867 60.000 0.00 0.00 37.10 3.28
2528 3089 0.537371 CGGCAGGTTTCCTCTTTGGT 60.537 55.000 0.00 0.00 37.07 3.67
2529 3090 0.961753 GGCAGGTTTCCTCTTTGGTG 59.038 55.000 0.00 0.00 37.07 4.17
2530 3091 0.315251 GCAGGTTTCCTCTTTGGTGC 59.685 55.000 0.00 0.00 37.07 5.01
2531 3092 1.986882 CAGGTTTCCTCTTTGGTGCT 58.013 50.000 0.00 0.00 37.07 4.40
2532 3093 2.814097 GCAGGTTTCCTCTTTGGTGCTA 60.814 50.000 0.00 0.00 37.07 3.49
2533 3094 3.486383 CAGGTTTCCTCTTTGGTGCTAA 58.514 45.455 0.00 0.00 37.07 3.09
2534 3095 4.082125 CAGGTTTCCTCTTTGGTGCTAAT 58.918 43.478 0.00 0.00 37.07 1.73
2535 3096 4.082125 AGGTTTCCTCTTTGGTGCTAATG 58.918 43.478 0.00 0.00 37.07 1.90
2536 3097 4.079253 GGTTTCCTCTTTGGTGCTAATGA 58.921 43.478 0.00 0.00 37.07 2.57
2537 3098 4.156739 GGTTTCCTCTTTGGTGCTAATGAG 59.843 45.833 4.85 4.85 37.07 2.90
2538 3099 3.634397 TCCTCTTTGGTGCTAATGAGG 57.366 47.619 17.96 17.96 45.96 3.86
2539 3100 2.019984 CCTCTTTGGTGCTAATGAGGC 58.980 52.381 14.07 0.00 41.88 4.70
2540 3101 2.618816 CCTCTTTGGTGCTAATGAGGCA 60.619 50.000 14.07 0.00 41.88 4.75
2541 3102 3.084039 CTCTTTGGTGCTAATGAGGCAA 58.916 45.455 0.00 0.00 41.54 4.52
2542 3103 3.084039 TCTTTGGTGCTAATGAGGCAAG 58.916 45.455 0.00 0.00 41.54 4.01
2543 3104 1.176527 TTGGTGCTAATGAGGCAAGC 58.823 50.000 0.00 0.00 41.54 4.01
2544 3105 1.026182 TGGTGCTAATGAGGCAAGCG 61.026 55.000 0.00 0.00 41.54 4.68
2545 3106 1.063166 GTGCTAATGAGGCAAGCGC 59.937 57.895 0.00 0.00 41.54 5.92
2546 3107 1.377072 TGCTAATGAGGCAAGCGCA 60.377 52.632 11.47 0.00 41.24 6.09
2547 3108 1.354506 GCTAATGAGGCAAGCGCAG 59.645 57.895 11.47 2.01 41.24 5.18
2548 3109 2.020131 CTAATGAGGCAAGCGCAGG 58.980 57.895 11.47 1.05 41.24 4.85
2549 3110 0.745845 CTAATGAGGCAAGCGCAGGT 60.746 55.000 11.47 0.00 41.24 4.00
2550 3111 1.026182 TAATGAGGCAAGCGCAGGTG 61.026 55.000 11.47 5.69 39.47 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 88 3.655777 TGGGGTTGAAGAGGACAGTAATT 59.344 43.478 0.00 0.00 0.00 1.40
89 91 2.409064 TGGGGTTGAAGAGGACAGTA 57.591 50.000 0.00 0.00 0.00 2.74
119 121 3.056821 GGTATGACAGTGTGCACTCACTA 60.057 47.826 19.41 0.00 45.37 2.74
122 124 1.001974 GGGTATGACAGTGTGCACTCA 59.998 52.381 19.41 13.58 40.20 3.41
162 164 5.718649 GCAATAGTGATAGCGACTGAAAA 57.281 39.130 0.00 0.00 0.00 2.29
172 174 1.000163 ACCCGAGCGCAATAGTGATAG 60.000 52.381 11.47 0.00 0.00 2.08
174 176 0.530650 CACCCGAGCGCAATAGTGAT 60.531 55.000 11.47 0.00 0.00 3.06
222 224 5.648092 TCGTGTTGTCAATGATCTCTCTCTA 59.352 40.000 0.00 0.00 0.00 2.43
272 274 1.348008 CCTGCTTGATCCTAGCCCCA 61.348 60.000 12.75 0.00 37.85 4.96
278 280 2.224821 CAGGCCCTGCTTGATCCTA 58.775 57.895 0.00 0.00 37.87 2.94
295 297 0.918799 TTTCTCCCCTATGGCCAGCA 60.919 55.000 13.05 0.00 0.00 4.41
305 307 2.846827 CCCTGAGTTGTATTTCTCCCCT 59.153 50.000 0.00 0.00 0.00 4.79
306 308 2.092375 CCCCTGAGTTGTATTTCTCCCC 60.092 54.545 0.00 0.00 0.00 4.81
324 327 5.601583 TTGGTTGACTTTTCTTTTACCCC 57.398 39.130 0.00 0.00 0.00 4.95
345 348 3.314541 AACGATCTCGGCAGTTACTTT 57.685 42.857 4.44 0.00 44.95 2.66
350 353 1.298859 GCCAAACGATCTCGGCAGTT 61.299 55.000 4.44 0.00 44.25 3.16
381 384 4.082081 CCAATTTAGGTGATTTCAGCAGCA 60.082 41.667 11.89 0.00 46.03 4.41
407 410 4.803426 CTCGCACGCTCAGGGTCC 62.803 72.222 0.00 0.00 0.00 4.46
462 465 2.006888 CACCATACCCGTCAATGTGAC 58.993 52.381 0.00 0.00 43.65 3.67
473 476 4.014406 CCAACTTTAACCTCACCATACCC 58.986 47.826 0.00 0.00 0.00 3.69
482 485 2.579410 TGGGCTCCAACTTTAACCTC 57.421 50.000 0.00 0.00 0.00 3.85
489 492 2.102578 GCACATATTGGGCTCCAACTT 58.897 47.619 8.59 0.00 46.95 2.66
548 551 7.932491 AGAGAGTTGGTACTTTTTCCTTAGTTC 59.068 37.037 0.00 0.00 33.84 3.01
574 577 1.403647 CGTGATTCACTACTCGGGCAA 60.404 52.381 14.54 0.00 31.34 4.52
585 588 0.109781 ATTTGCACCGCGTGATTCAC 60.110 50.000 4.92 6.73 35.23 3.18
607 610 5.562890 CGATCACGCCTTGAAGAGTATATCA 60.563 44.000 0.00 0.00 37.92 2.15
611 614 2.688446 TCGATCACGCCTTGAAGAGTAT 59.312 45.455 0.00 0.00 37.92 2.12
626 1033 2.202388 GCGACGTCGGTTCGATCA 60.202 61.111 36.13 0.00 38.42 2.92
764 1173 0.384230 CTCATTTCGTGCACGCGTTT 60.384 50.000 33.63 15.34 39.60 3.60
951 1369 6.213600 CCCTTTATATGCACACCTCTACCTAT 59.786 42.308 0.00 0.00 0.00 2.57
1013 1431 0.460987 CCAGATCGTCTCCTGGTTGC 60.461 60.000 0.00 0.00 43.71 4.17
1357 1784 3.213402 CCTCCTCCTCGTCTCCGC 61.213 72.222 0.00 0.00 0.00 5.54
1439 1866 1.332195 CAGATGGATCGGGCTAGACA 58.668 55.000 0.00 0.00 0.00 3.41
1440 1867 0.605589 CCAGATGGATCGGGCTAGAC 59.394 60.000 0.00 0.00 35.44 2.59
1441 1868 0.188587 ACCAGATGGATCGGGCTAGA 59.811 55.000 5.72 0.00 44.62 2.43
1447 1874 1.208052 ACAAGTGACCAGATGGATCGG 59.792 52.381 5.72 0.00 38.94 4.18
1462 1896 2.566833 TTAGCATCACAGCCACAAGT 57.433 45.000 0.00 0.00 34.23 3.16
1471 1905 4.445305 CCAAGAGGATGGATTAGCATCACA 60.445 45.833 0.00 0.00 43.54 3.58
1515 1949 0.247460 TTCTGGCTCCATGTGACTCG 59.753 55.000 0.00 0.00 0.00 4.18
1522 1956 5.587388 ACAACATTAATTCTGGCTCCATG 57.413 39.130 0.00 0.00 0.00 3.66
1562 1997 7.714377 TCTCTCAATCTCAAGAAAGATAATGCC 59.286 37.037 0.00 0.00 34.90 4.40
1708 2144 2.905075 GCAACTTGCAACTCCCTTTTT 58.095 42.857 8.97 0.00 44.26 1.94
1733 2169 3.570559 GCTCTACGTATGGATGAGCTTC 58.429 50.000 20.52 0.00 44.52 3.86
1795 2231 0.367210 GCTCGCTCGTTGCTTCTTAC 59.633 55.000 2.29 0.00 40.11 2.34
1805 2241 1.522806 AGATCTCTCGCTCGCTCGT 60.523 57.895 0.00 0.00 0.00 4.18
1880 2330 4.023107 TCTCGTTTACAAGAGTGACAGGAG 60.023 45.833 0.00 0.00 36.03 3.69
1938 2390 3.184581 GGATATTTGTTGGCGATCGAGTC 59.815 47.826 21.57 7.94 0.00 3.36
1940 2392 3.185188 CAGGATATTTGTTGGCGATCGAG 59.815 47.826 21.57 0.00 0.00 4.04
1972 2425 2.419673 TGAATCGTGTGCATGATTGGAC 59.580 45.455 20.36 9.71 44.53 4.02
2009 2462 4.707105 ACAACAGATATCGCCATCATCAA 58.293 39.130 0.00 0.00 0.00 2.57
2115 2568 0.523072 CGGTCTCCTTGCAAACCATG 59.477 55.000 16.30 0.00 0.00 3.66
2196 2734 1.899437 TTGCCTCGGACCATCACCTC 61.899 60.000 0.00 0.00 0.00 3.85
2219 2773 5.465390 CGAACTGGAGTACATGACAAAAGAA 59.535 40.000 0.00 0.00 0.00 2.52
2221 2775 4.988540 TCGAACTGGAGTACATGACAAAAG 59.011 41.667 0.00 0.00 0.00 2.27
2232 2787 1.170442 TGTGCGATCGAACTGGAGTA 58.830 50.000 26.09 2.52 0.00 2.59
2243 2798 4.946784 ATTTCCTGTAAGTTGTGCGATC 57.053 40.909 0.00 0.00 0.00 3.69
2275 2830 5.523438 TTTGTCAGTTTGGATGTTAACCC 57.477 39.130 2.48 0.00 0.00 4.11
2333 2893 8.306680 ACATAATTTTATCTACCGGTCGAATG 57.693 34.615 12.40 11.58 0.00 2.67
2365 2926 3.525537 CAGAATGCCGACAGTGTTAGAT 58.474 45.455 0.00 0.00 0.00 1.98
2366 2927 2.959516 CAGAATGCCGACAGTGTTAGA 58.040 47.619 0.00 0.00 0.00 2.10
2380 2941 1.369625 GTACCCTGGTTCGCAGAATG 58.630 55.000 0.00 0.00 45.90 2.67
2381 2942 0.252197 GGTACCCTGGTTCGCAGAAT 59.748 55.000 0.00 0.00 45.90 2.40
2382 2943 1.675219 GGTACCCTGGTTCGCAGAA 59.325 57.895 0.00 0.00 45.90 3.02
2383 2944 3.384348 GGTACCCTGGTTCGCAGA 58.616 61.111 0.00 0.00 0.00 4.26
2396 2957 0.036875 AAGCAGGCAAGTCTGGGTAC 59.963 55.000 3.62 0.00 35.43 3.34
2397 2958 1.278127 GTAAGCAGGCAAGTCTGGGTA 59.722 52.381 3.62 0.00 35.43 3.69
2398 2959 0.036875 GTAAGCAGGCAAGTCTGGGT 59.963 55.000 3.62 0.00 35.43 4.51
2399 2960 1.021390 CGTAAGCAGGCAAGTCTGGG 61.021 60.000 3.62 0.00 35.43 4.45
2400 2961 1.021390 CCGTAAGCAGGCAAGTCTGG 61.021 60.000 3.62 0.00 35.43 3.86
2401 2962 0.320771 ACCGTAAGCAGGCAAGTCTG 60.321 55.000 0.00 0.00 37.79 3.51
2402 2963 0.037232 GACCGTAAGCAGGCAAGTCT 60.037 55.000 0.00 0.00 0.00 3.24
2403 2964 1.019805 GGACCGTAAGCAGGCAAGTC 61.020 60.000 0.00 0.00 0.00 3.01
2404 2965 1.003718 GGACCGTAAGCAGGCAAGT 60.004 57.895 0.00 0.00 0.00 3.16
2405 2966 0.392998 ATGGACCGTAAGCAGGCAAG 60.393 55.000 0.00 0.00 0.00 4.01
2406 2967 0.676466 CATGGACCGTAAGCAGGCAA 60.676 55.000 0.00 0.00 0.00 4.52
2407 2968 1.078497 CATGGACCGTAAGCAGGCA 60.078 57.895 0.00 0.00 0.00 4.75
2408 2969 1.819632 CCATGGACCGTAAGCAGGC 60.820 63.158 5.56 0.00 0.00 4.85
2409 2970 1.819632 GCCATGGACCGTAAGCAGG 60.820 63.158 18.40 0.00 0.00 4.85
2410 2971 2.173669 CGCCATGGACCGTAAGCAG 61.174 63.158 18.40 0.00 0.00 4.24
2411 2972 2.125310 CGCCATGGACCGTAAGCA 60.125 61.111 18.40 0.00 0.00 3.91
2412 2973 2.125269 ACGCCATGGACCGTAAGC 60.125 61.111 18.40 0.00 35.69 3.09
2413 2974 3.794270 CACGCCATGGACCGTAAG 58.206 61.111 18.40 1.82 35.69 2.34
2422 2983 3.274586 CGATGGAGCCACGCCATG 61.275 66.667 7.62 0.00 43.71 3.66
2423 2984 3.469970 TCGATGGAGCCACGCCAT 61.470 61.111 2.26 2.26 46.19 4.40
2424 2985 4.451150 GTCGATGGAGCCACGCCA 62.451 66.667 0.00 0.00 37.78 5.69
2430 2991 4.899239 CAGGCCGTCGATGGAGCC 62.899 72.222 28.06 20.83 46.13 4.70
2431 2992 1.806461 TATCAGGCCGTCGATGGAGC 61.806 60.000 28.06 12.46 0.00 4.70
2432 2993 0.039074 GTATCAGGCCGTCGATGGAG 60.039 60.000 28.06 15.37 0.00 3.86
2433 2994 1.792118 CGTATCAGGCCGTCGATGGA 61.792 60.000 28.06 6.55 0.00 3.41
2434 2995 1.371758 CGTATCAGGCCGTCGATGG 60.372 63.158 19.87 19.87 0.00 3.51
2435 2996 1.371758 CCGTATCAGGCCGTCGATG 60.372 63.158 13.68 0.00 0.00 3.84
2436 2997 3.039988 CCGTATCAGGCCGTCGAT 58.960 61.111 9.82 9.82 0.00 3.59
2444 3005 1.121407 TGGAGATGGGCCGTATCAGG 61.121 60.000 21.13 0.00 0.00 3.86
2445 3006 0.758734 TTGGAGATGGGCCGTATCAG 59.241 55.000 21.13 0.00 0.00 2.90
2446 3007 0.468226 GTTGGAGATGGGCCGTATCA 59.532 55.000 21.13 6.85 0.00 2.15
2447 3008 0.250338 GGTTGGAGATGGGCCGTATC 60.250 60.000 12.00 12.00 0.00 2.24
2448 3009 0.986019 TGGTTGGAGATGGGCCGTAT 60.986 55.000 0.00 0.00 0.00 3.06
2449 3010 1.613928 TGGTTGGAGATGGGCCGTA 60.614 57.895 0.00 0.00 0.00 4.02
2450 3011 2.933287 TGGTTGGAGATGGGCCGT 60.933 61.111 0.00 0.00 0.00 5.68
2451 3012 2.124570 CTGGTTGGAGATGGGCCG 60.125 66.667 0.00 0.00 0.00 6.13
2452 3013 2.276740 CCTGGTTGGAGATGGGCC 59.723 66.667 0.00 0.00 38.35 5.80
2453 3014 3.415186 TCCTGGTTGGAGATGGGC 58.585 61.111 0.00 0.00 40.56 5.36
2460 3021 0.178992 CTTGCCTTGTCCTGGTTGGA 60.179 55.000 0.00 0.00 43.86 3.53
2461 3022 0.178992 TCTTGCCTTGTCCTGGTTGG 60.179 55.000 0.00 0.00 37.10 3.77
2462 3023 0.954452 GTCTTGCCTTGTCCTGGTTG 59.046 55.000 0.00 0.00 0.00 3.77
2463 3024 0.178990 GGTCTTGCCTTGTCCTGGTT 60.179 55.000 0.00 0.00 0.00 3.67
2464 3025 1.456287 GGTCTTGCCTTGTCCTGGT 59.544 57.895 0.00 0.00 0.00 4.00
2465 3026 1.303643 GGGTCTTGCCTTGTCCTGG 60.304 63.158 0.00 0.00 37.43 4.45
2466 3027 0.322008 GAGGGTCTTGCCTTGTCCTG 60.322 60.000 0.00 0.00 37.43 3.86
2467 3028 1.831652 CGAGGGTCTTGCCTTGTCCT 61.832 60.000 0.00 0.00 37.43 3.85
2468 3029 1.376037 CGAGGGTCTTGCCTTGTCC 60.376 63.158 0.00 0.00 37.43 4.02
2469 3030 2.035442 GCGAGGGTCTTGCCTTGTC 61.035 63.158 0.00 0.00 35.00 3.18
2470 3031 2.032681 GCGAGGGTCTTGCCTTGT 59.967 61.111 0.00 0.00 35.00 3.16
2471 3032 3.121030 CGCGAGGGTCTTGCCTTG 61.121 66.667 0.00 0.00 37.58 3.61
2472 3033 3.302347 CTCGCGAGGGTCTTGCCTT 62.302 63.158 28.40 0.00 37.58 4.35
2473 3034 3.764466 CTCGCGAGGGTCTTGCCT 61.764 66.667 28.40 0.00 37.58 4.75
2474 3035 4.821589 CCTCGCGAGGGTCTTGCC 62.822 72.222 41.47 0.00 44.87 4.52
2503 3064 3.435186 GGAAACCTGCCGCTCTGC 61.435 66.667 0.00 0.00 0.00 4.26
2504 3065 1.743252 GAGGAAACCTGCCGCTCTG 60.743 63.158 0.00 0.00 31.76 3.35
2505 3066 1.484444 AAGAGGAAACCTGCCGCTCT 61.484 55.000 0.00 0.00 34.28 4.09
2506 3067 0.606673 AAAGAGGAAACCTGCCGCTC 60.607 55.000 0.00 0.00 34.28 5.03
2507 3068 0.890996 CAAAGAGGAAACCTGCCGCT 60.891 55.000 0.00 0.00 37.13 5.52
2508 3069 1.581447 CAAAGAGGAAACCTGCCGC 59.419 57.895 0.00 0.00 31.76 6.53
2509 3070 0.537371 ACCAAAGAGGAAACCTGCCG 60.537 55.000 0.00 0.00 41.22 5.69
2510 3071 0.961753 CACCAAAGAGGAAACCTGCC 59.038 55.000 0.00 0.00 41.22 4.85
2511 3072 0.315251 GCACCAAAGAGGAAACCTGC 59.685 55.000 0.00 0.00 41.22 4.85
2512 3073 1.986882 AGCACCAAAGAGGAAACCTG 58.013 50.000 0.00 0.00 41.22 4.00
2513 3074 3.876309 TTAGCACCAAAGAGGAAACCT 57.124 42.857 0.00 0.00 41.22 3.50
2514 3075 4.079253 TCATTAGCACCAAAGAGGAAACC 58.921 43.478 0.00 0.00 41.22 3.27
2515 3076 4.156739 CCTCATTAGCACCAAAGAGGAAAC 59.843 45.833 9.98 0.00 44.12 2.78
2516 3077 4.335416 CCTCATTAGCACCAAAGAGGAAA 58.665 43.478 9.98 0.00 44.12 3.13
2517 3078 3.873801 GCCTCATTAGCACCAAAGAGGAA 60.874 47.826 16.53 0.00 44.12 3.36
2518 3079 2.356125 GCCTCATTAGCACCAAAGAGGA 60.356 50.000 16.53 0.00 44.12 3.71
2519 3080 2.019984 GCCTCATTAGCACCAAAGAGG 58.980 52.381 10.81 10.81 44.19 3.69
2520 3081 2.715046 TGCCTCATTAGCACCAAAGAG 58.285 47.619 0.00 0.00 34.69 2.85
2521 3082 2.877097 TGCCTCATTAGCACCAAAGA 57.123 45.000 0.00 0.00 34.69 2.52
2522 3083 2.416431 GCTTGCCTCATTAGCACCAAAG 60.416 50.000 0.00 0.00 40.69 2.77
2523 3084 1.545582 GCTTGCCTCATTAGCACCAAA 59.454 47.619 0.00 0.00 40.69 3.28
2524 3085 1.176527 GCTTGCCTCATTAGCACCAA 58.823 50.000 0.00 0.00 40.69 3.67
2525 3086 1.026182 CGCTTGCCTCATTAGCACCA 61.026 55.000 0.00 0.00 40.69 4.17
2526 3087 1.723870 CGCTTGCCTCATTAGCACC 59.276 57.895 0.00 0.00 40.69 5.01
2527 3088 1.063166 GCGCTTGCCTCATTAGCAC 59.937 57.895 0.00 0.00 40.69 4.40
2528 3089 1.371337 CTGCGCTTGCCTCATTAGCA 61.371 55.000 9.73 0.00 38.81 3.49
2529 3090 1.354506 CTGCGCTTGCCTCATTAGC 59.645 57.895 9.73 0.00 38.03 3.09
2530 3091 0.745845 ACCTGCGCTTGCCTCATTAG 60.746 55.000 9.73 0.00 38.03 1.73
2531 3092 1.026182 CACCTGCGCTTGCCTCATTA 61.026 55.000 9.73 0.00 38.03 1.90
2532 3093 2.034687 ACCTGCGCTTGCCTCATT 59.965 55.556 9.73 0.00 38.03 2.57
2533 3094 2.749044 CACCTGCGCTTGCCTCAT 60.749 61.111 9.73 0.00 38.03 2.90


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

AutoCloner maintained by Alex Coulton.