Multiple sequence alignment - TraesCS1B01G079200

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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 TraesCS1B01G079200 chr1B 100.000 2990 0 0 1 2990 61961054 61964043 0.000000e+00 5522.0
1 TraesCS1B01G079200 chr1B 79.032 124 20 5 1887 2008 62199074 62199193 2.470000e-11 80.5
2 TraesCS1B01G079200 chr1D 91.778 1350 80 13 966 2296 41820762 41822099 0.000000e+00 1849.0
3 TraesCS1B01G079200 chr1D 75.000 524 77 20 453 957 465547912 465547424 3.040000e-45 193.0
4 TraesCS1B01G079200 chr7B 100.000 965 0 0 1 965 348280974 348280010 0.000000e+00 1783.0
5 TraesCS1B01G079200 chr7B 97.000 100 2 1 2892 2990 67108705 67108606 1.840000e-37 167.0
6 TraesCS1B01G079200 chr3B 94.124 970 44 6 1 964 817223392 817222430 0.000000e+00 1463.0
7 TraesCS1B01G079200 chr3B 82.376 505 79 6 2372 2871 65551791 65551292 5.920000e-117 431.0
8 TraesCS1B01G079200 chr3B 100.000 90 0 0 2901 2990 302245691 302245602 1.840000e-37 167.0
9 TraesCS1B01G079200 chr3B 100.000 90 0 0 2901 2990 547671307 547671396 1.840000e-37 167.0
10 TraesCS1B01G079200 chr1A 86.058 1248 129 28 1669 2898 41873288 41874508 0.000000e+00 1299.0
11 TraesCS1B01G079200 chr1A 89.667 600 43 4 1008 1600 41872702 41873289 0.000000e+00 747.0
12 TraesCS1B01G079200 chr1A 82.812 512 73 13 2372 2876 372030384 372029881 7.610000e-121 444.0
13 TraesCS1B01G079200 chr1A 82.809 477 70 10 2400 2871 41831914 41831445 1.660000e-112 416.0
14 TraesCS1B01G079200 chr1A 84.211 114 11 7 1895 2008 41831308 41831414 1.470000e-18 104.0
15 TraesCS1B01G079200 chr6B 84.436 514 69 9 2363 2871 130327272 130326765 2.070000e-136 496.0
16 TraesCS1B01G079200 chr7D 82.540 504 73 12 2374 2871 12451464 12451958 2.130000e-116 429.0
17 TraesCS1B01G079200 chrUn 82.376 505 76 9 2375 2871 65973640 65974139 7.660000e-116 427.0
18 TraesCS1B01G079200 chrUn 98.889 90 1 0 2901 2990 6219123 6219212 8.580000e-36 161.0
19 TraesCS1B01G079200 chrUn 98.889 90 1 0 2901 2990 55883739 55883828 8.580000e-36 161.0
20 TraesCS1B01G079200 chrUn 98.889 90 1 0 2901 2990 61803215 61803126 8.580000e-36 161.0
21 TraesCS1B01G079200 chrUn 98.889 90 1 0 2901 2990 70286480 70286391 8.580000e-36 161.0
22 TraesCS1B01G079200 chrUn 98.889 90 1 0 2901 2990 86972926 86972837 8.580000e-36 161.0
23 TraesCS1B01G079200 chrUn 98.889 90 1 0 2901 2990 87274370 87274281 8.580000e-36 161.0
24 TraesCS1B01G079200 chr4D 82.863 496 66 16 2383 2871 469177952 469178435 7.660000e-116 427.0
25 TraesCS1B01G079200 chr5D 81.944 504 75 12 2373 2871 522762278 522762770 2.140000e-111 412.0
26 TraesCS1B01G079200 chr4B 81.262 507 75 16 2372 2871 588908661 588909154 2.790000e-105 392.0
27 TraesCS1B01G079200 chr2D 81.148 122 10 8 4 120 328164584 328164471 5.310000e-13 86.1


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 TraesCS1B01G079200 chr1B 61961054 61964043 2989 False 5522 5522 100.0000 1 2990 1 chr1B.!!$F1 2989
1 TraesCS1B01G079200 chr1D 41820762 41822099 1337 False 1849 1849 91.7780 966 2296 1 chr1D.!!$F1 1330
2 TraesCS1B01G079200 chr7B 348280010 348280974 964 True 1783 1783 100.0000 1 965 1 chr7B.!!$R2 964
3 TraesCS1B01G079200 chr3B 817222430 817223392 962 True 1463 1463 94.1240 1 964 1 chr3B.!!$R3 963
4 TraesCS1B01G079200 chr1A 41872702 41874508 1806 False 1023 1299 87.8625 1008 2898 2 chr1A.!!$F2 1890
5 TraesCS1B01G079200 chr1A 372029881 372030384 503 True 444 444 82.8120 2372 2876 1 chr1A.!!$R2 504
6 TraesCS1B01G079200 chr6B 130326765 130327272 507 True 496 496 84.4360 2363 2871 1 chr6B.!!$R1 508

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
969 976 3.119245 TCACCTGATACTTCGCCTTGTAC 60.119 47.826 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2910 2955 0.033796 CCACCATCCTCCTGCAACAT 60.034 55.0 0.0 0.0 0.0 2.71 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
969 976 3.119245 TCACCTGATACTTCGCCTTGTAC 60.119 47.826 0.00 0.00 0.00 2.90
972 979 4.894114 ACCTGATACTTCGCCTTGTACTAT 59.106 41.667 0.00 0.00 0.00 2.12
976 983 3.166489 ACTTCGCCTTGTACTATCAGC 57.834 47.619 0.00 0.00 0.00 4.26
985 992 3.313012 TGTACTATCAGCGCAACACTT 57.687 42.857 11.47 0.00 0.00 3.16
986 993 3.659786 TGTACTATCAGCGCAACACTTT 58.340 40.909 11.47 0.00 0.00 2.66
1010 1017 4.380531 CACTTGCACCTCGTCCATATATT 58.619 43.478 0.00 0.00 0.00 1.28
1013 1020 4.681074 TGCACCTCGTCCATATATTGAA 57.319 40.909 0.00 0.00 0.00 2.69
1015 1022 3.428870 GCACCTCGTCCATATATTGAACG 59.571 47.826 5.38 5.38 0.00 3.95
1021 1028 4.340097 TCGTCCATATATTGAACGTCCAGT 59.660 41.667 9.74 0.00 0.00 4.00
1040 1047 1.669115 CCAGGCCACACTTCAGTCG 60.669 63.158 5.01 0.00 0.00 4.18
1106 1116 0.106708 GATGGCACGCCTATCTTCCA 59.893 55.000 9.92 0.00 36.94 3.53
1191 1201 2.026822 GTCAAGAGGAAGGAGGCATCAA 60.027 50.000 0.00 0.00 0.00 2.57
1227 1237 2.357517 AACCAAGGAGCAGTCGCG 60.358 61.111 0.00 0.00 45.49 5.87
1396 1406 3.490759 CGCATCGAGTTTGGCGCT 61.491 61.111 7.64 0.00 43.14 5.92
1479 1496 2.684843 GCGCTGCTTGCTTGCTACT 61.685 57.895 0.00 0.00 40.11 2.57
1485 1502 3.529533 CTGCTTGCTTGCTACTACTCAT 58.470 45.455 3.47 0.00 0.00 2.90
1518 1535 0.550914 TTTCACTTCTGGGGTGCAGT 59.449 50.000 0.00 0.00 34.97 4.40
1519 1536 0.550914 TTCACTTCTGGGGTGCAGTT 59.449 50.000 0.00 0.00 34.97 3.16
1520 1537 0.550914 TCACTTCTGGGGTGCAGTTT 59.449 50.000 0.00 0.00 34.97 2.66
1521 1538 1.064017 TCACTTCTGGGGTGCAGTTTT 60.064 47.619 0.00 0.00 34.97 2.43
1522 1539 1.067516 CACTTCTGGGGTGCAGTTTTG 59.932 52.381 0.00 0.00 0.00 2.44
1535 1552 3.629855 TGCAGTTTTGGAAGAATCGTTGA 59.370 39.130 0.00 0.00 0.00 3.18
1581 1598 1.413767 CGTCCAAGGCGAACGATGAG 61.414 60.000 0.00 0.00 38.65 2.90
1653 1670 3.623060 CCTTGTCGATGAACGGAATTGAT 59.377 43.478 0.00 0.00 42.82 2.57
1656 1673 5.966636 TGTCGATGAACGGAATTGATAAG 57.033 39.130 0.00 0.00 42.82 1.73
1756 1773 1.475280 AGTAGCTTGTTATGGCGTCGA 59.525 47.619 0.00 0.00 0.00 4.20
1783 1800 2.494677 AGGTTCGTCCTCGGAGATG 58.505 57.895 6.58 0.00 44.42 2.90
1803 1823 9.081997 GGAGATGTTATCGAATTCATCATCTAC 57.918 37.037 20.65 16.89 39.96 2.59
1834 1854 4.041723 GTGATTGTGGTTTATTATGCGGC 58.958 43.478 0.00 0.00 0.00 6.53
1855 1875 2.700773 GGCGTGGTCTCCATTTGCC 61.701 63.158 11.62 11.62 40.16 4.52
1860 1880 0.896923 TGGTCTCCATTTGCCATTGC 59.103 50.000 0.00 0.00 38.26 3.56
1918 1939 5.708948 TCCTGCAAATTCCTGTAAAAATCG 58.291 37.500 0.00 0.00 0.00 3.34
2057 2081 8.548025 TCATAGAATGTCAAGTTTTATGGGAGA 58.452 33.333 0.00 0.00 29.47 3.71
2064 2088 6.107343 GTCAAGTTTTATGGGAGAGAGGTAC 58.893 44.000 0.00 0.00 0.00 3.34
2120 2144 4.221482 AGAAAAAGGGAAACATGATGGAGC 59.779 41.667 0.00 0.00 0.00 4.70
2204 2228 3.379057 ACAACCCTTTTACCGTGAAACAG 59.621 43.478 0.00 0.00 35.74 3.16
2247 2273 2.223066 CCGAGTACTGACGAGCAACTAG 60.223 54.545 0.00 0.00 0.00 2.57
2296 2322 2.834549 AGGTGGTGGTACTTCTCATGAG 59.165 50.000 17.07 17.07 0.00 2.90
2297 2323 2.567615 GGTGGTGGTACTTCTCATGAGT 59.432 50.000 21.92 6.96 0.00 3.41
2298 2324 3.368531 GGTGGTGGTACTTCTCATGAGTC 60.369 52.174 21.92 8.80 0.00 3.36
2299 2325 3.258372 GTGGTGGTACTTCTCATGAGTCA 59.742 47.826 21.92 9.56 0.00 3.41
2300 2326 4.081420 GTGGTGGTACTTCTCATGAGTCAT 60.081 45.833 21.92 10.89 0.00 3.06
2301 2327 4.081476 TGGTGGTACTTCTCATGAGTCATG 60.081 45.833 24.60 24.60 42.60 3.07
2302 2328 4.160439 GGTGGTACTTCTCATGAGTCATGA 59.840 45.833 29.39 29.39 46.84 3.07
2319 2345 2.462456 TGACATGAGACAGTTGAGGC 57.538 50.000 0.00 0.00 0.00 4.70
2320 2346 1.693606 TGACATGAGACAGTTGAGGCA 59.306 47.619 0.00 0.00 0.00 4.75
2321 2347 2.289257 TGACATGAGACAGTTGAGGCAG 60.289 50.000 0.00 0.00 0.00 4.85
2322 2348 1.973515 ACATGAGACAGTTGAGGCAGA 59.026 47.619 0.00 0.00 0.00 4.26
2323 2349 2.289320 ACATGAGACAGTTGAGGCAGAC 60.289 50.000 0.00 0.00 0.00 3.51
2324 2350 0.315251 TGAGACAGTTGAGGCAGACG 59.685 55.000 0.00 0.00 0.00 4.18
2325 2351 1.005630 AGACAGTTGAGGCAGACGC 60.006 57.895 0.00 0.00 37.44 5.19
2326 2352 1.005630 GACAGTTGAGGCAGACGCT 60.006 57.895 0.00 0.00 38.60 5.07
2341 2373 2.787915 GCTCAAAGTAGCGCCAGC 59.212 61.111 2.29 0.00 45.58 4.85
2352 2384 1.296649 GCGCCAGCGATTCGTAAAC 60.297 57.895 17.53 0.00 42.83 2.01
2353 2385 1.347221 CGCCAGCGATTCGTAAACC 59.653 57.895 6.06 0.00 42.83 3.27
2357 2389 1.330521 CCAGCGATTCGTAAACCATGG 59.669 52.381 11.19 11.19 0.00 3.66
2358 2390 1.014352 AGCGATTCGTAAACCATGGC 58.986 50.000 13.04 0.00 0.00 4.40
2359 2391 0.315869 GCGATTCGTAAACCATGGCG 60.316 55.000 13.04 7.47 0.00 5.69
2360 2392 0.303493 CGATTCGTAAACCATGGCGG 59.697 55.000 13.04 0.00 42.50 6.13
2361 2393 1.658994 GATTCGTAAACCATGGCGGA 58.341 50.000 13.04 1.60 38.63 5.54
2363 2395 2.116827 TTCGTAAACCATGGCGGAAT 57.883 45.000 13.04 0.00 38.63 3.01
2364 2396 2.983907 TCGTAAACCATGGCGGAATA 57.016 45.000 13.04 0.00 38.63 1.75
2365 2397 3.478857 TCGTAAACCATGGCGGAATAT 57.521 42.857 13.04 0.00 38.63 1.28
2380 2412 5.697633 GGCGGAATATTACTACGGAAATTCA 59.302 40.000 0.00 0.00 0.00 2.57
2381 2413 6.370718 GGCGGAATATTACTACGGAAATTCAT 59.629 38.462 0.00 0.00 0.00 2.57
2405 2437 1.378514 CAAGTAAGTGCGGGGGCAT 60.379 57.895 0.00 0.00 0.00 4.40
2442 2477 2.100631 CGTCCGCTCGATTTGCCTT 61.101 57.895 0.00 0.00 0.00 4.35
2444 2479 1.019278 GTCCGCTCGATTTGCCTTGA 61.019 55.000 0.00 0.00 0.00 3.02
2450 2485 2.679837 GCTCGATTTGCCTTGAGATTCA 59.320 45.455 0.00 0.00 0.00 2.57
2467 2502 7.331026 TGAGATTCACGAAGTAATTGAATCCT 58.669 34.615 16.26 7.28 43.07 3.24
2469 2504 6.540189 AGATTCACGAAGTAATTGAATCCTGG 59.460 38.462 16.26 0.00 43.07 4.45
2470 2505 3.938963 TCACGAAGTAATTGAATCCTGGC 59.061 43.478 0.00 0.00 41.61 4.85
2553 2595 8.207545 ACAGTTTTTACATCTAAAAATGCCCAA 58.792 29.630 8.00 0.00 41.60 4.12
2569 2611 5.033589 TGCCCAATTTCAACAAGTTTCAT 57.966 34.783 0.00 0.00 0.00 2.57
2572 2614 6.183360 TGCCCAATTTCAACAAGTTTCATAGT 60.183 34.615 0.00 0.00 0.00 2.12
2608 2651 3.529634 TTTTTATGTTGGTCGCACGAG 57.470 42.857 0.00 0.00 0.00 4.18
2609 2652 2.157834 TTTATGTTGGTCGCACGAGT 57.842 45.000 0.00 0.00 0.00 4.18
2620 2663 3.615496 GGTCGCACGAGTACACAAAATAT 59.385 43.478 0.00 0.00 0.00 1.28
2819 2864 9.198837 GAAAATCGGAAGCCAAAATAAAAAGTA 57.801 29.630 0.00 0.00 0.00 2.24
2871 2916 1.684983 CATGCCACAAATCCTCATCCC 59.315 52.381 0.00 0.00 0.00 3.85
2873 2918 1.288633 TGCCACAAATCCTCATCCCAT 59.711 47.619 0.00 0.00 0.00 4.00
2882 2927 8.378565 CACAAATCCTCATCCCATATTACTAGT 58.621 37.037 0.00 0.00 0.00 2.57
2918 2963 2.906691 TTTTGGGGTCAATGTTGCAG 57.093 45.000 0.00 0.00 32.28 4.41
2919 2964 1.047002 TTTGGGGTCAATGTTGCAGG 58.953 50.000 0.00 0.00 32.28 4.85
2920 2965 0.187117 TTGGGGTCAATGTTGCAGGA 59.813 50.000 0.00 0.00 0.00 3.86
2921 2966 0.251297 TGGGGTCAATGTTGCAGGAG 60.251 55.000 0.00 0.00 0.00 3.69
2922 2967 0.967380 GGGGTCAATGTTGCAGGAGG 60.967 60.000 0.00 0.00 0.00 4.30
2923 2968 0.038166 GGGTCAATGTTGCAGGAGGA 59.962 55.000 0.00 0.00 0.00 3.71
2924 2969 1.341383 GGGTCAATGTTGCAGGAGGAT 60.341 52.381 0.00 0.00 0.00 3.24
2925 2970 1.747355 GGTCAATGTTGCAGGAGGATG 59.253 52.381 0.00 0.00 0.00 3.51
2926 2971 1.747355 GTCAATGTTGCAGGAGGATGG 59.253 52.381 0.00 0.00 0.00 3.51
2927 2972 1.355381 TCAATGTTGCAGGAGGATGGT 59.645 47.619 0.00 0.00 0.00 3.55
2928 2973 1.475280 CAATGTTGCAGGAGGATGGTG 59.525 52.381 0.00 0.00 0.00 4.17
2929 2974 0.033796 ATGTTGCAGGAGGATGGTGG 60.034 55.000 0.00 0.00 0.00 4.61
2930 2975 1.380302 GTTGCAGGAGGATGGTGGT 59.620 57.895 0.00 0.00 0.00 4.16
2931 2976 0.618458 GTTGCAGGAGGATGGTGGTA 59.382 55.000 0.00 0.00 0.00 3.25
2932 2977 1.212935 GTTGCAGGAGGATGGTGGTAT 59.787 52.381 0.00 0.00 0.00 2.73
2933 2978 1.595311 TGCAGGAGGATGGTGGTATT 58.405 50.000 0.00 0.00 0.00 1.89
2934 2979 1.212688 TGCAGGAGGATGGTGGTATTG 59.787 52.381 0.00 0.00 0.00 1.90
2935 2980 1.490490 GCAGGAGGATGGTGGTATTGA 59.510 52.381 0.00 0.00 0.00 2.57
2936 2981 2.107204 GCAGGAGGATGGTGGTATTGAT 59.893 50.000 0.00 0.00 0.00 2.57
2937 2982 3.748083 CAGGAGGATGGTGGTATTGATG 58.252 50.000 0.00 0.00 0.00 3.07
2938 2983 3.392285 CAGGAGGATGGTGGTATTGATGA 59.608 47.826 0.00 0.00 0.00 2.92
2939 2984 4.047166 AGGAGGATGGTGGTATTGATGAA 58.953 43.478 0.00 0.00 0.00 2.57
2940 2985 4.103785 AGGAGGATGGTGGTATTGATGAAG 59.896 45.833 0.00 0.00 0.00 3.02
2941 2986 4.103153 GGAGGATGGTGGTATTGATGAAGA 59.897 45.833 0.00 0.00 0.00 2.87
2942 2987 5.222007 GGAGGATGGTGGTATTGATGAAGAT 60.222 44.000 0.00 0.00 0.00 2.40
2943 2988 5.628130 AGGATGGTGGTATTGATGAAGATG 58.372 41.667 0.00 0.00 0.00 2.90
2944 2989 5.133322 AGGATGGTGGTATTGATGAAGATGT 59.867 40.000 0.00 0.00 0.00 3.06
2945 2990 5.240183 GGATGGTGGTATTGATGAAGATGTG 59.760 44.000 0.00 0.00 0.00 3.21
2946 2991 5.434182 TGGTGGTATTGATGAAGATGTGA 57.566 39.130 0.00 0.00 0.00 3.58
2947 2992 5.814481 TGGTGGTATTGATGAAGATGTGAA 58.186 37.500 0.00 0.00 0.00 3.18
2948 2993 5.647658 TGGTGGTATTGATGAAGATGTGAAC 59.352 40.000 0.00 0.00 0.00 3.18
2949 2994 5.066505 GGTGGTATTGATGAAGATGTGAACC 59.933 44.000 0.00 0.00 0.00 3.62
2950 2995 5.647658 GTGGTATTGATGAAGATGTGAACCA 59.352 40.000 0.00 0.00 0.00 3.67
2951 2996 6.319658 GTGGTATTGATGAAGATGTGAACCAT 59.680 38.462 0.00 0.00 35.86 3.55
2962 3007 3.829886 TGTGAACCATCGAATCAAAGC 57.170 42.857 0.00 0.00 0.00 3.51
2963 3008 2.487762 TGTGAACCATCGAATCAAAGCC 59.512 45.455 0.00 0.00 0.00 4.35
2964 3009 1.737236 TGAACCATCGAATCAAAGCCG 59.263 47.619 0.00 0.00 0.00 5.52
2965 3010 1.064060 GAACCATCGAATCAAAGCCGG 59.936 52.381 0.00 0.00 0.00 6.13
2966 3011 0.251916 ACCATCGAATCAAAGCCGGA 59.748 50.000 5.05 0.00 0.00 5.14
2967 3012 1.134098 ACCATCGAATCAAAGCCGGAT 60.134 47.619 5.05 0.00 0.00 4.18
2968 3013 1.265095 CCATCGAATCAAAGCCGGATG 59.735 52.381 5.05 0.00 0.00 3.51
2969 3014 1.265095 CATCGAATCAAAGCCGGATGG 59.735 52.381 5.05 0.00 38.77 3.51
2970 3015 0.539518 TCGAATCAAAGCCGGATGGA 59.460 50.000 5.05 0.00 37.49 3.41
2971 3016 1.140852 TCGAATCAAAGCCGGATGGAT 59.859 47.619 5.05 2.85 37.49 3.41
2972 3017 1.265095 CGAATCAAAGCCGGATGGATG 59.735 52.381 5.05 0.00 37.49 3.51
2973 3018 2.575532 GAATCAAAGCCGGATGGATGA 58.424 47.619 5.05 5.46 37.49 2.92
2974 3019 2.734755 ATCAAAGCCGGATGGATGAA 57.265 45.000 5.05 0.00 37.49 2.57
2975 3020 2.042686 TCAAAGCCGGATGGATGAAG 57.957 50.000 5.05 0.00 37.49 3.02
2976 3021 1.281867 TCAAAGCCGGATGGATGAAGT 59.718 47.619 5.05 0.00 37.49 3.01
2977 3022 1.402968 CAAAGCCGGATGGATGAAGTG 59.597 52.381 5.05 0.00 37.49 3.16
2978 3023 0.107017 AAGCCGGATGGATGAAGTGG 60.107 55.000 5.05 0.00 37.49 4.00
2979 3024 2.189499 GCCGGATGGATGAAGTGGC 61.189 63.158 5.05 0.00 37.49 5.01
2980 3025 1.889105 CCGGATGGATGAAGTGGCG 60.889 63.158 0.00 0.00 37.49 5.69
2981 3026 2.537560 CGGATGGATGAAGTGGCGC 61.538 63.158 0.00 0.00 0.00 6.53
2982 3027 2.189499 GGATGGATGAAGTGGCGCC 61.189 63.158 22.73 22.73 0.00 6.53
2983 3028 1.451927 GATGGATGAAGTGGCGCCA 60.452 57.895 29.03 29.03 0.00 5.69
2984 3029 1.001020 ATGGATGAAGTGGCGCCAA 60.001 52.632 34.66 17.35 31.53 4.52
2985 3030 1.033746 ATGGATGAAGTGGCGCCAAG 61.034 55.000 34.66 0.00 31.53 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
990 997 4.631131 TCAATATATGGACGAGGTGCAAG 58.369 43.478 0.00 0.00 37.44 4.01
992 999 4.377021 GTTCAATATATGGACGAGGTGCA 58.623 43.478 0.00 0.00 38.41 4.57
993 1000 4.992381 GTTCAATATATGGACGAGGTGC 57.008 45.455 0.00 0.00 0.00 5.01
1010 1017 2.741092 GCCTGGACTGGACGTTCA 59.259 61.111 0.00 0.00 0.00 3.18
1013 1020 3.626924 GTGGCCTGGACTGGACGT 61.627 66.667 3.32 0.00 38.15 4.34
1015 1022 2.032681 GTGTGGCCTGGACTGGAC 59.967 66.667 3.32 0.00 35.14 4.02
1021 1028 1.754745 GACTGAAGTGTGGCCTGGA 59.245 57.895 3.32 0.00 0.00 3.86
1040 1047 3.369451 GCGGAGAGATGTTCTGTTTCTTC 59.631 47.826 0.00 0.00 35.87 2.87
1106 1116 0.029267 AGCAGGAGGGAGATGGGAAT 60.029 55.000 0.00 0.00 0.00 3.01
1167 1177 1.201429 GCCTCCTTCCTCTTGACCCA 61.201 60.000 0.00 0.00 0.00 4.51
1170 1180 1.556911 TGATGCCTCCTTCCTCTTGAC 59.443 52.381 0.00 0.00 0.00 3.18
1207 1217 1.371183 CGACTGCTCCTTGGTTGGA 59.629 57.895 0.00 0.00 34.52 3.53
1255 1265 2.735772 GCCGGATCCTTGAGCCTGA 61.736 63.158 5.05 0.00 35.75 3.86
1395 1405 2.022764 TGCAACATACGGATGGTCAG 57.977 50.000 13.36 0.00 37.39 3.51
1396 1406 2.560504 GATGCAACATACGGATGGTCA 58.439 47.619 13.36 6.42 37.39 4.02
1485 1502 8.469200 CCCAGAAGTGAAATTTAATAAGCATGA 58.531 33.333 0.00 0.00 0.00 3.07
1503 1520 1.402787 CAAAACTGCACCCCAGAAGT 58.597 50.000 0.00 0.00 44.64 3.01
1518 1535 4.082787 GCATCCTCAACGATTCTTCCAAAA 60.083 41.667 0.00 0.00 0.00 2.44
1519 1536 3.440173 GCATCCTCAACGATTCTTCCAAA 59.560 43.478 0.00 0.00 0.00 3.28
1520 1537 3.009723 GCATCCTCAACGATTCTTCCAA 58.990 45.455 0.00 0.00 0.00 3.53
1521 1538 2.632377 GCATCCTCAACGATTCTTCCA 58.368 47.619 0.00 0.00 0.00 3.53
1522 1539 1.943340 GGCATCCTCAACGATTCTTCC 59.057 52.381 0.00 0.00 0.00 3.46
1622 1639 1.078759 CATCGACAAGGACACGAGGC 61.079 60.000 0.00 0.00 39.31 4.70
1653 1670 0.548031 CTTGCTGCCATCCTCCCTTA 59.452 55.000 0.00 0.00 0.00 2.69
1656 1673 2.123982 CCTTGCTGCCATCCTCCC 60.124 66.667 0.00 0.00 0.00 4.30
1756 1773 1.980844 GGACGAACCTTACTGGCCT 59.019 57.895 3.32 0.00 40.22 5.19
1766 1783 0.531200 AACATCTCCGAGGACGAACC 59.469 55.000 0.00 0.00 42.66 3.62
1803 1823 4.836125 AAACCACAATCACTGCAACTAG 57.164 40.909 0.00 0.00 0.00 2.57
1855 1875 0.232816 GGCAACAAACAAGCGCAATG 59.767 50.000 11.47 11.29 0.00 2.82
1860 1880 6.472163 CCTTTATATTAGGCAACAAACAAGCG 59.528 38.462 0.00 0.00 41.41 4.68
1949 1970 8.928448 TGCTTTACTAAGATCAACATCCTAGAT 58.072 33.333 0.00 0.00 32.92 1.98
1955 1976 9.282247 CACATTTGCTTTACTAAGATCAACATC 57.718 33.333 0.00 0.00 32.92 3.06
2033 2057 8.772250 TCTCTCCCATAAAACTTGACATTCTAT 58.228 33.333 0.00 0.00 0.00 1.98
2057 2081 5.864418 TGTCTTTGTTGTGTAGTACCTCT 57.136 39.130 0.00 0.00 0.00 3.69
2064 2088 6.656314 TGTACAGTTGTCTTTGTTGTGTAG 57.344 37.500 0.00 0.00 0.00 2.74
2163 2187 2.096466 TGTTCACTATTTTCACAGCGCG 60.096 45.455 0.00 0.00 0.00 6.86
2204 2228 6.202188 TCGGTACAAAGTTCAAACAGATTCTC 59.798 38.462 0.00 0.00 0.00 2.87
2247 2273 2.288334 TGTGTTGAATGCATGTGGCTTC 60.288 45.455 0.00 0.00 45.15 3.86
2296 2322 3.931468 CCTCAACTGTCTCATGTCATGAC 59.069 47.826 19.27 19.27 35.06 3.06
2297 2323 3.618263 GCCTCAACTGTCTCATGTCATGA 60.618 47.826 14.76 14.76 37.76 3.07
2298 2324 2.676839 GCCTCAACTGTCTCATGTCATG 59.323 50.000 6.47 6.47 0.00 3.07
2299 2325 2.303890 TGCCTCAACTGTCTCATGTCAT 59.696 45.455 0.00 0.00 0.00 3.06
2300 2326 1.693606 TGCCTCAACTGTCTCATGTCA 59.306 47.619 0.00 0.00 0.00 3.58
2301 2327 2.028658 TCTGCCTCAACTGTCTCATGTC 60.029 50.000 0.00 0.00 0.00 3.06
2302 2328 1.973515 TCTGCCTCAACTGTCTCATGT 59.026 47.619 0.00 0.00 0.00 3.21
2324 2350 2.787915 GCTGGCGCTACTTTGAGC 59.212 61.111 7.64 0.00 39.20 4.26
2325 2351 0.807667 ATCGCTGGCGCTACTTTGAG 60.808 55.000 7.64 0.00 39.59 3.02
2326 2352 0.391130 AATCGCTGGCGCTACTTTGA 60.391 50.000 7.64 0.00 39.59 2.69
2341 2373 0.303493 CCGCCATGGTTTACGAATCG 59.697 55.000 14.67 0.00 0.00 3.34
2346 2378 4.753107 AGTAATATTCCGCCATGGTTTACG 59.247 41.667 14.67 8.10 39.52 3.18
2352 2384 3.056393 TCCGTAGTAATATTCCGCCATGG 60.056 47.826 7.63 7.63 40.09 3.66
2353 2385 4.182693 TCCGTAGTAATATTCCGCCATG 57.817 45.455 0.00 0.00 0.00 3.66
2357 2389 6.774354 TGAATTTCCGTAGTAATATTCCGC 57.226 37.500 0.00 0.00 0.00 5.54
2358 2390 9.084164 CCTATGAATTTCCGTAGTAATATTCCG 57.916 37.037 0.00 0.00 0.00 4.30
2359 2391 9.379791 CCCTATGAATTTCCGTAGTAATATTCC 57.620 37.037 0.00 0.00 0.00 3.01
2360 2392 9.379791 CCCCTATGAATTTCCGTAGTAATATTC 57.620 37.037 0.00 0.00 0.00 1.75
2361 2393 7.827729 GCCCCTATGAATTTCCGTAGTAATATT 59.172 37.037 0.00 0.00 0.00 1.28
2363 2395 6.270463 TGCCCCTATGAATTTCCGTAGTAATA 59.730 38.462 0.00 0.00 0.00 0.98
2364 2396 5.072600 TGCCCCTATGAATTTCCGTAGTAAT 59.927 40.000 0.00 0.00 0.00 1.89
2365 2397 4.409574 TGCCCCTATGAATTTCCGTAGTAA 59.590 41.667 0.00 0.00 0.00 2.24
2380 2412 0.180406 CCGCACTTACTTGCCCCTAT 59.820 55.000 0.00 0.00 39.53 2.57
2381 2413 1.600107 CCGCACTTACTTGCCCCTA 59.400 57.895 0.00 0.00 39.53 3.53
2405 2437 2.115910 CAGGGCTTGGCAGGTGAA 59.884 61.111 0.00 0.00 0.00 3.18
2426 2461 0.740868 CTCAAGGCAAATCGAGCGGA 60.741 55.000 0.00 0.00 0.00 5.54
2450 2485 3.279434 GGCCAGGATTCAATTACTTCGT 58.721 45.455 0.00 0.00 0.00 3.85
2536 2578 7.222872 TGTTGAAATTGGGCATTTTTAGATGT 58.777 30.769 0.00 0.00 35.02 3.06
2593 2636 0.315886 TGTACTCGTGCGACCAACAT 59.684 50.000 0.00 0.00 0.00 2.71
2597 2640 0.102663 TTTGTGTACTCGTGCGACCA 59.897 50.000 0.00 0.00 0.00 4.02
2636 2679 6.220930 TCAATGTTGAAACTTAGTACGAGCT 58.779 36.000 0.00 0.00 33.55 4.09
2779 2824 8.612619 GCTTCCGATTTTCAAAGTTCTATATCA 58.387 33.333 0.00 0.00 0.00 2.15
2819 2864 1.462238 ACTCAGGTCCCTTGTGCCT 60.462 57.895 0.00 0.00 0.00 4.75
2846 2891 0.899720 AGGATTTGTGGCATGCAAGG 59.100 50.000 21.36 0.00 0.00 3.61
2852 2897 1.288633 TGGGATGAGGATTTGTGGCAT 59.711 47.619 0.00 0.00 0.00 4.40
2857 2902 8.511748 ACTAGTAATATGGGATGAGGATTTGT 57.488 34.615 0.00 0.00 0.00 2.83
2898 2943 2.158842 CCTGCAACATTGACCCCAAAAA 60.159 45.455 0.00 0.00 35.67 1.94
2899 2944 1.415659 CCTGCAACATTGACCCCAAAA 59.584 47.619 0.00 0.00 35.67 2.44
2900 2945 1.047002 CCTGCAACATTGACCCCAAA 58.953 50.000 0.00 0.00 35.67 3.28
2901 2946 0.187117 TCCTGCAACATTGACCCCAA 59.813 50.000 0.00 0.00 36.61 4.12
2902 2947 0.251297 CTCCTGCAACATTGACCCCA 60.251 55.000 0.00 0.00 0.00 4.96
2903 2948 0.967380 CCTCCTGCAACATTGACCCC 60.967 60.000 0.00 0.00 0.00 4.95
2904 2949 0.038166 TCCTCCTGCAACATTGACCC 59.962 55.000 0.00 0.00 0.00 4.46
2905 2950 1.747355 CATCCTCCTGCAACATTGACC 59.253 52.381 0.00 0.00 0.00 4.02
2906 2951 1.747355 CCATCCTCCTGCAACATTGAC 59.253 52.381 0.00 0.00 0.00 3.18
2907 2952 1.355381 ACCATCCTCCTGCAACATTGA 59.645 47.619 0.00 0.00 0.00 2.57
2908 2953 1.475280 CACCATCCTCCTGCAACATTG 59.525 52.381 0.00 0.00 0.00 2.82
2909 2954 1.617804 CCACCATCCTCCTGCAACATT 60.618 52.381 0.00 0.00 0.00 2.71
2910 2955 0.033796 CCACCATCCTCCTGCAACAT 60.034 55.000 0.00 0.00 0.00 2.71
2911 2956 1.379916 CCACCATCCTCCTGCAACA 59.620 57.895 0.00 0.00 0.00 3.33
2912 2957 0.618458 TACCACCATCCTCCTGCAAC 59.382 55.000 0.00 0.00 0.00 4.17
2913 2958 1.595311 ATACCACCATCCTCCTGCAA 58.405 50.000 0.00 0.00 0.00 4.08
2914 2959 1.212688 CAATACCACCATCCTCCTGCA 59.787 52.381 0.00 0.00 0.00 4.41
2915 2960 1.490490 TCAATACCACCATCCTCCTGC 59.510 52.381 0.00 0.00 0.00 4.85
2916 2961 3.392285 TCATCAATACCACCATCCTCCTG 59.608 47.826 0.00 0.00 0.00 3.86
2917 2962 3.668821 TCATCAATACCACCATCCTCCT 58.331 45.455 0.00 0.00 0.00 3.69
2918 2963 4.103153 TCTTCATCAATACCACCATCCTCC 59.897 45.833 0.00 0.00 0.00 4.30
2919 2964 5.296151 TCTTCATCAATACCACCATCCTC 57.704 43.478 0.00 0.00 0.00 3.71
2920 2965 5.133322 ACATCTTCATCAATACCACCATCCT 59.867 40.000 0.00 0.00 0.00 3.24
2921 2966 5.240183 CACATCTTCATCAATACCACCATCC 59.760 44.000 0.00 0.00 0.00 3.51
2922 2967 6.057533 TCACATCTTCATCAATACCACCATC 58.942 40.000 0.00 0.00 0.00 3.51
2923 2968 6.005066 TCACATCTTCATCAATACCACCAT 57.995 37.500 0.00 0.00 0.00 3.55
2924 2969 5.434182 TCACATCTTCATCAATACCACCA 57.566 39.130 0.00 0.00 0.00 4.17
2925 2970 5.066505 GGTTCACATCTTCATCAATACCACC 59.933 44.000 0.00 0.00 0.00 4.61
2926 2971 5.647658 TGGTTCACATCTTCATCAATACCAC 59.352 40.000 0.00 0.00 0.00 4.16
2927 2972 5.814481 TGGTTCACATCTTCATCAATACCA 58.186 37.500 0.00 0.00 0.00 3.25
2928 2973 6.949352 ATGGTTCACATCTTCATCAATACC 57.051 37.500 0.00 0.00 33.53 2.73
2941 2986 3.129287 GGCTTTGATTCGATGGTTCACAT 59.871 43.478 0.00 0.00 44.18 3.21
2942 2987 2.487762 GGCTTTGATTCGATGGTTCACA 59.512 45.455 0.00 0.00 0.00 3.58
2943 2988 2.476185 CGGCTTTGATTCGATGGTTCAC 60.476 50.000 0.00 0.00 0.00 3.18
2944 2989 1.737236 CGGCTTTGATTCGATGGTTCA 59.263 47.619 0.00 0.00 0.00 3.18
2945 2990 1.064060 CCGGCTTTGATTCGATGGTTC 59.936 52.381 0.00 0.00 0.00 3.62
2946 2991 1.094785 CCGGCTTTGATTCGATGGTT 58.905 50.000 0.00 0.00 0.00 3.67
2947 2992 0.251916 TCCGGCTTTGATTCGATGGT 59.748 50.000 0.00 0.00 0.00 3.55
2948 2993 1.265095 CATCCGGCTTTGATTCGATGG 59.735 52.381 0.00 0.00 0.00 3.51
2949 2994 1.265095 CCATCCGGCTTTGATTCGATG 59.735 52.381 0.00 0.00 0.00 3.84
2950 2995 1.140852 TCCATCCGGCTTTGATTCGAT 59.859 47.619 0.00 0.00 0.00 3.59
2951 2996 0.539518 TCCATCCGGCTTTGATTCGA 59.460 50.000 0.00 0.00 0.00 3.71
2952 2997 1.265095 CATCCATCCGGCTTTGATTCG 59.735 52.381 0.00 0.00 0.00 3.34
2953 2998 2.575532 TCATCCATCCGGCTTTGATTC 58.424 47.619 0.00 0.00 0.00 2.52
2954 2999 2.734755 TCATCCATCCGGCTTTGATT 57.265 45.000 0.00 0.00 0.00 2.57
2955 3000 2.092212 ACTTCATCCATCCGGCTTTGAT 60.092 45.455 0.00 0.00 0.00 2.57
2956 3001 1.281867 ACTTCATCCATCCGGCTTTGA 59.718 47.619 0.00 0.00 0.00 2.69
2957 3002 1.402968 CACTTCATCCATCCGGCTTTG 59.597 52.381 0.00 0.00 0.00 2.77
2958 3003 1.683011 CCACTTCATCCATCCGGCTTT 60.683 52.381 0.00 0.00 0.00 3.51
2959 3004 0.107017 CCACTTCATCCATCCGGCTT 60.107 55.000 0.00 0.00 0.00 4.35
2960 3005 1.528824 CCACTTCATCCATCCGGCT 59.471 57.895 0.00 0.00 0.00 5.52
2961 3006 2.189499 GCCACTTCATCCATCCGGC 61.189 63.158 0.00 0.00 0.00 6.13
2962 3007 1.889105 CGCCACTTCATCCATCCGG 60.889 63.158 0.00 0.00 0.00 5.14
2963 3008 2.537560 GCGCCACTTCATCCATCCG 61.538 63.158 0.00 0.00 0.00 4.18
2964 3009 2.189499 GGCGCCACTTCATCCATCC 61.189 63.158 24.80 0.00 0.00 3.51
2965 3010 1.031571 TTGGCGCCACTTCATCCATC 61.032 55.000 32.95 0.00 0.00 3.51
2966 3011 1.001020 TTGGCGCCACTTCATCCAT 60.001 52.632 32.95 0.00 0.00 3.41
2967 3012 1.675310 CTTGGCGCCACTTCATCCA 60.675 57.895 32.95 11.39 0.00 3.41
2968 3013 3.056313 GCTTGGCGCCACTTCATCC 62.056 63.158 32.95 8.49 0.00 3.51
2969 3014 1.589716 AAGCTTGGCGCCACTTCATC 61.590 55.000 32.95 10.52 40.39 2.92
2970 3015 1.589716 GAAGCTTGGCGCCACTTCAT 61.590 55.000 36.48 22.40 38.68 2.57
2971 3016 2.203337 AAGCTTGGCGCCACTTCA 60.203 55.556 32.95 14.51 40.39 3.02
2972 3017 2.563427 GAAGCTTGGCGCCACTTC 59.437 61.111 31.94 31.94 40.39 3.01


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

AutoCloner maintained by Alex Coulton.