Multiple sequence alignment - TraesCS4D01G300300

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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 TraesCS4D01G300300 chr4D 100.000 3065 0 0 1 3065 468824450 468827514 0.000000e+00 5661.0
1 TraesCS4D01G300300 chr4D 95.322 962 43 2 1 961 468818883 468819843 0.000000e+00 1526.0
2 TraesCS4D01G300300 chr4D 95.480 885 40 0 1999 2883 468854358 468855242 0.000000e+00 1413.0
3 TraesCS4D01G300300 chr7D 95.021 964 41 5 1 961 620310087 620311046 0.000000e+00 1507.0
4 TraesCS4D01G300300 chr7D 93.182 968 58 6 1 962 24388073 24389038 0.000000e+00 1415.0
5 TraesCS4D01G300300 chr7D 94.273 908 51 1 1999 2905 422785463 422786370 0.000000e+00 1387.0
6 TraesCS4D01G300300 chr7D 98.788 165 2 0 2901 3065 394701064 394700900 8.310000e-76 294.0
7 TraesCS4D01G300300 chr7D 99.379 161 1 0 2905 3065 503176589 503176429 2.990000e-75 292.0
8 TraesCS4D01G300300 chr1D 94.595 962 49 3 1 961 383912094 383911135 0.000000e+00 1485.0
9 TraesCS4D01G300300 chr1D 94.093 965 54 3 1 964 383917661 383916699 0.000000e+00 1463.0
10 TraesCS4D01G300300 chr1D 94.176 910 52 1 1998 2907 286564068 286564976 0.000000e+00 1386.0
11 TraesCS4D01G300300 chr4B 91.817 1051 80 5 952 1998 588578872 588579920 0.000000e+00 1459.0
12 TraesCS4D01G300300 chr4B 91.532 1051 83 5 952 1998 588546948 588547996 0.000000e+00 1443.0
13 TraesCS4D01G300300 chr6D 93.905 968 53 5 1 962 420954869 420955836 0.000000e+00 1456.0
14 TraesCS4D01G300300 chr6D 97.093 172 4 1 2895 3065 289181555 289181384 3.870000e-74 289.0
15 TraesCS4D01G300300 chr3D 93.971 962 52 4 1 961 608499391 608500347 0.000000e+00 1450.0
16 TraesCS4D01G300300 chr3D 94.396 910 50 1 1998 2906 86433444 86434353 0.000000e+00 1397.0
17 TraesCS4D01G300300 chr3D 93.791 918 55 2 1990 2906 297937774 297938690 0.000000e+00 1378.0
18 TraesCS4D01G300300 chr5D 95.028 905 43 2 2003 2906 318987451 318988354 0.000000e+00 1421.0
19 TraesCS4D01G300300 chr5D 94.396 910 49 2 1999 2906 262216316 262215407 0.000000e+00 1397.0
20 TraesCS4D01G300300 chr5D 94.169 909 51 2 1999 2906 279051033 279050126 0.000000e+00 1384.0
21 TraesCS4D01G300300 chr5A 93.139 962 65 1 1 961 547248220 547249181 0.000000e+00 1410.0
22 TraesCS4D01G300300 chr5A 94.536 183 5 4 2886 3065 404356807 404356987 8.370000e-71 278.0
23 TraesCS4D01G300300 chr2D 94.396 910 50 1 1998 2906 495766393 495767302 0.000000e+00 1397.0
24 TraesCS4D01G300300 chr2D 98.193 166 1 2 2900 3065 374265957 374266120 3.870000e-74 289.0
25 TraesCS4D01G300300 chr3A 92.827 962 68 1 1 961 445229584 445228623 0.000000e+00 1393.0
26 TraesCS4D01G300300 chr4A 86.708 978 79 13 1003 1977 2781036 2780107 0.000000e+00 1038.0
27 TraesCS4D01G300300 chr1B 83.547 468 50 19 2604 3065 476571752 476571306 2.200000e-111 412.0
28 TraesCS4D01G300300 chr1B 94.022 184 6 5 2882 3065 83398410 83398588 1.080000e-69 274.0
29 TraesCS4D01G300300 chr5B 98.773 163 2 0 2903 3065 587705791 587705953 1.080000e-74 291.0
30 TraesCS4D01G300300 chr3B 96.532 173 3 3 2893 3065 173630736 173630905 1.800000e-72 283.0
31 TraesCS4D01G300300 chr7A 76.101 159 32 5 1004 1158 643645180 643645336 9.110000e-11 78.7
32 TraesCS4D01G300300 chr7B 75.472 159 34 4 1004 1158 606142594 606142751 4.240000e-09 73.1


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 TraesCS4D01G300300 chr4D 468824450 468827514 3064 False 5661 5661 100.000 1 3065 1 chr4D.!!$F2 3064
1 TraesCS4D01G300300 chr4D 468818883 468819843 960 False 1526 1526 95.322 1 961 1 chr4D.!!$F1 960
2 TraesCS4D01G300300 chr4D 468854358 468855242 884 False 1413 1413 95.480 1999 2883 1 chr4D.!!$F3 884
3 TraesCS4D01G300300 chr7D 620310087 620311046 959 False 1507 1507 95.021 1 961 1 chr7D.!!$F3 960
4 TraesCS4D01G300300 chr7D 24388073 24389038 965 False 1415 1415 93.182 1 962 1 chr7D.!!$F1 961
5 TraesCS4D01G300300 chr7D 422785463 422786370 907 False 1387 1387 94.273 1999 2905 1 chr7D.!!$F2 906
6 TraesCS4D01G300300 chr1D 383911135 383912094 959 True 1485 1485 94.595 1 961 1 chr1D.!!$R1 960
7 TraesCS4D01G300300 chr1D 383916699 383917661 962 True 1463 1463 94.093 1 964 1 chr1D.!!$R2 963
8 TraesCS4D01G300300 chr1D 286564068 286564976 908 False 1386 1386 94.176 1998 2907 1 chr1D.!!$F1 909
9 TraesCS4D01G300300 chr4B 588578872 588579920 1048 False 1459 1459 91.817 952 1998 1 chr4B.!!$F2 1046
10 TraesCS4D01G300300 chr4B 588546948 588547996 1048 False 1443 1443 91.532 952 1998 1 chr4B.!!$F1 1046
11 TraesCS4D01G300300 chr6D 420954869 420955836 967 False 1456 1456 93.905 1 962 1 chr6D.!!$F1 961
12 TraesCS4D01G300300 chr3D 608499391 608500347 956 False 1450 1450 93.971 1 961 1 chr3D.!!$F3 960
13 TraesCS4D01G300300 chr3D 86433444 86434353 909 False 1397 1397 94.396 1998 2906 1 chr3D.!!$F1 908
14 TraesCS4D01G300300 chr3D 297937774 297938690 916 False 1378 1378 93.791 1990 2906 1 chr3D.!!$F2 916
15 TraesCS4D01G300300 chr5D 318987451 318988354 903 False 1421 1421 95.028 2003 2906 1 chr5D.!!$F1 903
16 TraesCS4D01G300300 chr5D 262215407 262216316 909 True 1397 1397 94.396 1999 2906 1 chr5D.!!$R1 907
17 TraesCS4D01G300300 chr5D 279050126 279051033 907 True 1384 1384 94.169 1999 2906 1 chr5D.!!$R2 907
18 TraesCS4D01G300300 chr5A 547248220 547249181 961 False 1410 1410 93.139 1 961 1 chr5A.!!$F2 960
19 TraesCS4D01G300300 chr2D 495766393 495767302 909 False 1397 1397 94.396 1998 2906 1 chr2D.!!$F2 908
20 TraesCS4D01G300300 chr3A 445228623 445229584 961 True 1393 1393 92.827 1 961 1 chr3A.!!$R1 960
21 TraesCS4D01G300300 chr4A 2780107 2781036 929 True 1038 1038 86.708 1003 1977 1 chr4A.!!$R1 974

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
714 727 3.005539 ATGGCTGGCGAGGACACT 61.006 61.111 0.0 0.0 0.0 3.55 F
1181 1198 0.176680 AGCTCAGATGACGCCGATTT 59.823 50.000 0.0 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 1697 0.990374 AGATGAAGTGGAGCAAGGCT 59.010 50.0 0.0 0.0 43.88 4.58 R
3016 3039 0.043334 AGTAGGAGCCCACCACATCT 59.957 55.0 0.0 0.0 0.00 2.90 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
255 267 4.134563 GCACGATGGGTATATGAAAGGTT 58.865 43.478 0.00 0.00 0.00 3.50
370 382 4.753662 ACCTCCCGTCGCAGCCTA 62.754 66.667 0.00 0.00 0.00 3.93
714 727 3.005539 ATGGCTGGCGAGGACACT 61.006 61.111 0.00 0.00 0.00 3.55
971 984 8.421249 TTCATATTTCCAACACTCTTTTCCAT 57.579 30.769 0.00 0.00 0.00 3.41
1104 1121 1.072331 ACCGGCAAGTTCATCAAGTCT 59.928 47.619 0.00 0.00 0.00 3.24
1181 1198 0.176680 AGCTCAGATGACGCCGATTT 59.823 50.000 0.00 0.00 0.00 2.17
1182 1199 0.579156 GCTCAGATGACGCCGATTTC 59.421 55.000 0.00 0.00 0.00 2.17
1191 1208 3.738982 TGACGCCGATTTCATATCCATT 58.261 40.909 0.00 0.00 0.00 3.16
1192 1209 4.888917 TGACGCCGATTTCATATCCATTA 58.111 39.130 0.00 0.00 0.00 1.90
1205 1222 7.916914 TCATATCCATTAATCTACGTCTCGA 57.083 36.000 0.00 0.00 0.00 4.04
1273 1290 0.461870 CGATCAGCACGGGGAATCAA 60.462 55.000 0.00 0.00 0.00 2.57
1300 1317 1.131126 CATACAGCAACGAAAGCCAGG 59.869 52.381 0.00 0.00 0.00 4.45
1311 1328 0.611896 AAAGCCAGGTATGCGCCTTT 60.612 50.000 4.18 1.07 36.58 3.11
1329 1346 4.020485 GCCTTTAGAGTAACAGAAGGACCA 60.020 45.833 4.72 0.00 39.33 4.02
1368 1385 2.045926 CGCAAGGACTTGGAGGGG 60.046 66.667 13.41 0.00 40.74 4.79
1398 1415 2.996249 TGAGGGATGATGTCTTGAGC 57.004 50.000 0.00 0.00 0.00 4.26
1571 1591 2.661840 TTTCCCGCGCACAGGTACAA 62.662 55.000 8.75 0.00 0.00 2.41
1642 1662 1.503818 GGAAAAGACCGCAACTCGCA 61.504 55.000 0.00 0.00 42.60 5.10
1654 1674 3.666638 CGCAACTCGCATACAAATCAACA 60.667 43.478 0.00 0.00 42.60 3.33
1677 1697 2.655090 TGGATGCCAAAGTGTTCAGA 57.345 45.000 0.00 0.00 0.00 3.27
1710 1730 5.171476 CACTTCATCTACACCGACTCATTT 58.829 41.667 0.00 0.00 0.00 2.32
1725 1745 3.131933 ACTCATTTCCAGAGATGGACGAG 59.868 47.826 12.60 12.60 37.76 4.18
1728 1748 0.041238 TTCCAGAGATGGACGAGGGT 59.959 55.000 0.00 0.00 37.76 4.34
1732 1752 1.032657 AGAGATGGACGAGGGTGACG 61.033 60.000 0.00 0.00 0.00 4.35
1754 1774 4.970621 GGTGATGGCTCAGCATCA 57.029 55.556 0.00 3.21 46.77 3.07
1788 1808 1.409064 GACAGGTATGACATGGAGCGA 59.591 52.381 0.00 0.00 33.62 4.93
1802 1822 1.678627 GGAGCGACTCAAGCTGATCTA 59.321 52.381 8.71 0.00 46.13 1.98
1814 1834 1.974265 CTGATCTACGAGGAGAGGCA 58.026 55.000 0.00 0.00 0.00 4.75
1848 1868 1.672030 CAGAAGCATGGTGGCGACA 60.672 57.895 0.00 0.00 39.27 4.35
1856 1876 3.656045 GGTGGCGACAACGTTGGG 61.656 66.667 30.34 22.12 46.06 4.12
1872 1892 2.517875 GGATTGGCCGAGCAGCAT 60.518 61.111 11.15 0.00 0.00 3.79
1896 1916 2.359230 GGTGCGCTCAAGAAGGCT 60.359 61.111 9.73 0.00 0.00 4.58
1984 2004 4.486503 GGAGCAGCTGCCCCTCTG 62.487 72.222 34.39 0.00 43.38 3.35
2012 2032 0.534203 GAGTTTGTTGGCGTCCTGGA 60.534 55.000 0.00 0.00 0.00 3.86
2372 2392 0.249911 GGTGCAACGAGACCAAGACT 60.250 55.000 0.00 0.00 38.12 3.24
2414 2434 3.665675 ATCGTGGAGCCCAAGACGC 62.666 63.158 10.94 0.00 43.94 5.19
2496 2516 1.152355 CCCCCTTCAAACTTGCCCA 60.152 57.895 0.00 0.00 0.00 5.36
2581 2603 0.908180 GCCACCACAGTAGTAGGGGT 60.908 60.000 0.00 0.00 0.00 4.95
2591 2613 4.012374 CAGTAGTAGGGGTACTCGAACAA 58.988 47.826 0.00 0.00 0.00 2.83
2829 2851 2.176889 CGGTAGGAGGGAAAGACTTCA 58.823 52.381 0.00 0.00 32.75 3.02
2907 2930 4.992982 TGCCAGGTAGGGGTGCCA 62.993 66.667 0.00 0.00 38.09 4.92
2908 2931 4.426313 GCCAGGTAGGGGTGCCAC 62.426 72.222 0.00 0.00 38.09 5.01
2909 2932 2.610859 CCAGGTAGGGGTGCCACT 60.611 66.667 0.00 0.00 0.00 4.00
2910 2933 1.306654 CCAGGTAGGGGTGCCACTA 60.307 63.158 0.00 0.00 0.00 2.74
2911 2934 1.623542 CCAGGTAGGGGTGCCACTAC 61.624 65.000 19.57 19.57 39.01 2.73
2912 2935 0.907704 CAGGTAGGGGTGCCACTACA 60.908 60.000 26.36 0.00 40.96 2.74
2913 2936 0.178885 AGGTAGGGGTGCCACTACAA 60.179 55.000 26.36 0.00 40.96 2.41
2914 2937 0.694196 GGTAGGGGTGCCACTACAAA 59.306 55.000 26.36 0.00 40.96 2.83
2915 2938 1.074244 GGTAGGGGTGCCACTACAAAA 59.926 52.381 26.36 0.00 40.96 2.44
2916 2939 2.489437 GGTAGGGGTGCCACTACAAAAA 60.489 50.000 26.36 0.00 40.96 1.94
2937 2960 5.514274 AAAAAGACACATCCGTGACATTT 57.486 34.783 0.00 0.00 46.80 2.32
2938 2961 5.514274 AAAAGACACATCCGTGACATTTT 57.486 34.783 0.00 1.58 46.80 1.82
2939 2962 4.488126 AAGACACATCCGTGACATTTTG 57.512 40.909 0.00 0.00 46.80 2.44
2940 2963 2.813754 AGACACATCCGTGACATTTTGG 59.186 45.455 0.00 0.00 46.80 3.28
2941 2964 1.885887 ACACATCCGTGACATTTTGGG 59.114 47.619 0.00 0.00 46.80 4.12
2942 2965 0.887933 ACATCCGTGACATTTTGGGC 59.112 50.000 0.00 0.00 0.00 5.36
2943 2966 0.173255 CATCCGTGACATTTTGGGCC 59.827 55.000 0.00 0.00 0.00 5.80
2944 2967 1.312371 ATCCGTGACATTTTGGGCCG 61.312 55.000 0.00 0.00 0.00 6.13
2945 2968 1.969064 CCGTGACATTTTGGGCCGA 60.969 57.895 0.00 0.00 0.00 5.54
2946 2969 1.519751 CCGTGACATTTTGGGCCGAA 61.520 55.000 0.79 0.79 0.00 4.30
2947 2970 0.386731 CGTGACATTTTGGGCCGAAC 60.387 55.000 5.46 0.00 0.00 3.95
2948 2971 0.386731 GTGACATTTTGGGCCGAACG 60.387 55.000 5.46 3.01 0.00 3.95
2949 2972 0.535328 TGACATTTTGGGCCGAACGA 60.535 50.000 5.46 0.00 0.00 3.85
2950 2973 0.594110 GACATTTTGGGCCGAACGAA 59.406 50.000 5.46 0.00 0.00 3.85
2951 2974 1.201414 GACATTTTGGGCCGAACGAAT 59.799 47.619 5.46 0.00 0.00 3.34
2952 2975 1.616374 ACATTTTGGGCCGAACGAATT 59.384 42.857 5.46 0.00 0.00 2.17
2953 2976 2.036604 ACATTTTGGGCCGAACGAATTT 59.963 40.909 5.46 0.00 0.00 1.82
2954 2977 2.892784 TTTTGGGCCGAACGAATTTT 57.107 40.000 5.46 0.00 0.00 1.82
2955 2978 2.892784 TTTGGGCCGAACGAATTTTT 57.107 40.000 0.79 0.00 0.00 1.94
2986 3009 6.729187 TCATACAGATGACACTTCTATGACG 58.271 40.000 0.00 0.00 37.15 4.35
2987 3010 6.542370 TCATACAGATGACACTTCTATGACGA 59.458 38.462 0.00 0.00 37.15 4.20
2988 3011 5.843673 ACAGATGACACTTCTATGACGAT 57.156 39.130 0.00 0.00 0.00 3.73
2989 3012 6.944234 ACAGATGACACTTCTATGACGATA 57.056 37.500 0.00 0.00 0.00 2.92
2990 3013 7.334844 ACAGATGACACTTCTATGACGATAA 57.665 36.000 0.00 0.00 0.00 1.75
2991 3014 7.946207 ACAGATGACACTTCTATGACGATAAT 58.054 34.615 0.00 0.00 0.00 1.28
2992 3015 8.417106 ACAGATGACACTTCTATGACGATAATT 58.583 33.333 0.00 0.00 0.00 1.40
2993 3016 8.697960 CAGATGACACTTCTATGACGATAATTG 58.302 37.037 0.00 0.00 0.00 2.32
2994 3017 8.417106 AGATGACACTTCTATGACGATAATTGT 58.583 33.333 0.00 0.00 0.00 2.71
2995 3018 7.755582 TGACACTTCTATGACGATAATTGTG 57.244 36.000 0.00 0.00 0.00 3.33
2996 3019 7.543756 TGACACTTCTATGACGATAATTGTGA 58.456 34.615 0.00 0.00 0.00 3.58
2997 3020 7.488150 TGACACTTCTATGACGATAATTGTGAC 59.512 37.037 0.00 0.00 0.00 3.67
2998 3021 7.320399 ACACTTCTATGACGATAATTGTGACA 58.680 34.615 0.00 0.00 0.00 3.58
2999 3022 7.817478 ACACTTCTATGACGATAATTGTGACAA 59.183 33.333 0.00 0.00 0.00 3.18
3000 3023 8.655970 CACTTCTATGACGATAATTGTGACAAA 58.344 33.333 0.62 0.00 0.00 2.83
3001 3024 9.214957 ACTTCTATGACGATAATTGTGACAAAA 57.785 29.630 0.62 0.00 0.00 2.44
3002 3025 9.478019 CTTCTATGACGATAATTGTGACAAAAC 57.522 33.333 0.62 0.00 0.00 2.43
3003 3026 7.970384 TCTATGACGATAATTGTGACAAAACC 58.030 34.615 0.62 0.00 0.00 3.27
3004 3027 5.365403 TGACGATAATTGTGACAAAACCC 57.635 39.130 0.62 0.00 0.00 4.11
3005 3028 4.083749 TGACGATAATTGTGACAAAACCCG 60.084 41.667 0.62 7.01 0.00 5.28
3006 3029 3.189702 ACGATAATTGTGACAAAACCCGG 59.810 43.478 0.62 0.00 0.00 5.73
3007 3030 3.189702 CGATAATTGTGACAAAACCCGGT 59.810 43.478 0.62 0.00 0.00 5.28
3008 3031 4.392445 CGATAATTGTGACAAAACCCGGTA 59.608 41.667 0.62 0.00 0.00 4.02
3009 3032 5.065474 CGATAATTGTGACAAAACCCGGTAT 59.935 40.000 0.62 0.00 0.00 2.73
3010 3033 4.776795 AATTGTGACAAAACCCGGTATC 57.223 40.909 0.62 0.00 0.00 2.24
3011 3034 2.932855 TGTGACAAAACCCGGTATCA 57.067 45.000 0.00 0.00 0.00 2.15
3012 3035 3.426787 TGTGACAAAACCCGGTATCAT 57.573 42.857 0.00 0.00 0.00 2.45
3013 3036 3.340034 TGTGACAAAACCCGGTATCATC 58.660 45.455 0.00 0.00 0.00 2.92
3014 3037 3.244596 TGTGACAAAACCCGGTATCATCA 60.245 43.478 0.00 0.00 0.00 3.07
3015 3038 3.945285 GTGACAAAACCCGGTATCATCAT 59.055 43.478 0.00 0.00 0.00 2.45
3016 3039 5.120399 GTGACAAAACCCGGTATCATCATA 58.880 41.667 0.00 0.00 0.00 2.15
3017 3040 5.236478 GTGACAAAACCCGGTATCATCATAG 59.764 44.000 0.00 0.00 0.00 2.23
3018 3041 5.129650 TGACAAAACCCGGTATCATCATAGA 59.870 40.000 0.00 0.00 0.00 1.98
3019 3042 6.183361 TGACAAAACCCGGTATCATCATAGAT 60.183 38.462 0.00 0.00 0.00 1.98
3020 3043 5.997746 ACAAAACCCGGTATCATCATAGATG 59.002 40.000 0.00 0.62 0.00 2.90
3021 3044 5.825593 AAACCCGGTATCATCATAGATGT 57.174 39.130 0.00 0.00 0.00 3.06
3022 3045 4.808414 ACCCGGTATCATCATAGATGTG 57.192 45.455 0.00 0.00 0.00 3.21
3023 3046 3.515502 ACCCGGTATCATCATAGATGTGG 59.484 47.826 0.00 3.53 0.00 4.17
3024 3047 3.515502 CCCGGTATCATCATAGATGTGGT 59.484 47.826 0.00 0.00 0.00 4.16
3025 3048 4.498241 CCGGTATCATCATAGATGTGGTG 58.502 47.826 6.86 0.00 0.00 4.17
3026 3049 4.498241 CGGTATCATCATAGATGTGGTGG 58.502 47.826 6.86 0.00 0.00 4.61
3027 3050 4.621510 CGGTATCATCATAGATGTGGTGGG 60.622 50.000 6.86 0.00 0.00 4.61
3028 3051 2.936919 TCATCATAGATGTGGTGGGC 57.063 50.000 6.86 0.00 0.00 5.36
3029 3052 2.411583 TCATCATAGATGTGGTGGGCT 58.588 47.619 6.86 0.00 0.00 5.19
3030 3053 2.369860 TCATCATAGATGTGGTGGGCTC 59.630 50.000 6.86 0.00 0.00 4.70
3031 3054 1.131638 TCATAGATGTGGTGGGCTCC 58.868 55.000 0.00 0.00 0.00 4.70
3032 3055 1.135094 CATAGATGTGGTGGGCTCCT 58.865 55.000 0.00 0.00 0.00 3.69
3033 3056 2.090775 TCATAGATGTGGTGGGCTCCTA 60.091 50.000 0.00 0.00 0.00 2.94
3034 3057 1.789523 TAGATGTGGTGGGCTCCTAC 58.210 55.000 0.00 0.00 0.00 3.18
3035 3058 0.043334 AGATGTGGTGGGCTCCTACT 59.957 55.000 2.46 0.00 0.00 2.57
3036 3059 0.912486 GATGTGGTGGGCTCCTACTT 59.088 55.000 2.46 0.00 0.00 2.24
3037 3060 0.912486 ATGTGGTGGGCTCCTACTTC 59.088 55.000 2.46 0.00 0.00 3.01
3038 3061 0.178903 TGTGGTGGGCTCCTACTTCT 60.179 55.000 2.46 0.00 0.00 2.85
3039 3062 1.078159 TGTGGTGGGCTCCTACTTCTA 59.922 52.381 2.46 0.00 0.00 2.10
3040 3063 2.292918 TGTGGTGGGCTCCTACTTCTAT 60.293 50.000 2.46 0.00 0.00 1.98
3041 3064 2.103263 GTGGTGGGCTCCTACTTCTATG 59.897 54.545 2.46 0.00 0.00 2.23
3042 3065 2.023404 TGGTGGGCTCCTACTTCTATGA 60.023 50.000 2.46 0.00 0.00 2.15
3043 3066 2.365941 GGTGGGCTCCTACTTCTATGAC 59.634 54.545 2.46 0.00 0.00 3.06
3044 3067 3.031736 GTGGGCTCCTACTTCTATGACA 58.968 50.000 0.00 0.00 0.00 3.58
3045 3068 3.451178 GTGGGCTCCTACTTCTATGACAA 59.549 47.826 0.00 0.00 0.00 3.18
3046 3069 4.081087 GTGGGCTCCTACTTCTATGACAAA 60.081 45.833 0.00 0.00 0.00 2.83
3047 3070 4.534500 TGGGCTCCTACTTCTATGACAAAA 59.466 41.667 0.00 0.00 0.00 2.44
3048 3071 5.013704 TGGGCTCCTACTTCTATGACAAAAA 59.986 40.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 212 0.104487 AGACATCAGCTCGGCTCATG 59.896 55.000 7.92 7.92 42.73 3.07
212 224 4.233789 GCGTGGCAAAAATTTAGACATCA 58.766 39.130 2.78 0.00 0.00 3.07
255 267 0.036765 AATGTTTCAGCTCCCGCGTA 60.037 50.000 4.92 0.00 42.32 4.42
329 341 1.593196 CAACAAAGGGAGACGAAGCA 58.407 50.000 0.00 0.00 0.00 3.91
370 382 0.539051 CACAGGAGAAGGAGGCGAAT 59.461 55.000 0.00 0.00 0.00 3.34
477 489 0.038159 GGATGGGGAAGATCGTAGCG 60.038 60.000 0.00 0.00 0.00 4.26
507 519 0.036732 GTCCCAATCTGCAGTGGACA 59.963 55.000 27.12 13.39 43.92 4.02
510 522 0.037303 ACTGTCCCAATCTGCAGTGG 59.963 55.000 14.67 14.84 40.24 4.00
519 531 1.338136 CGGAGGCCTACTGTCCCAAT 61.338 60.000 14.69 0.00 0.00 3.16
548 560 3.170717 TCTCCCGTACAGGACTCAAAAT 58.829 45.455 0.00 0.00 45.00 1.82
714 727 3.948719 GCACCGGTCTTGGGGTCA 61.949 66.667 2.59 0.00 33.77 4.02
971 984 0.179084 CCGCCGCCAATCTTAGAAGA 60.179 55.000 0.00 0.00 39.78 2.87
1053 1070 3.755628 GTGCGGGAGTAGCCGTCA 61.756 66.667 0.00 0.00 37.63 4.35
1059 1076 2.584608 CCCTTGGTGCGGGAGTAG 59.415 66.667 0.00 0.00 44.90 2.57
1082 1099 1.238439 CTTGATGAACTTGCCGGTGT 58.762 50.000 1.90 0.00 0.00 4.16
1163 1180 0.579156 GAAATCGGCGTCATCTGAGC 59.421 55.000 6.85 0.00 0.00 4.26
1181 1198 7.916914 TCGAGACGTAGATTAATGGATATGA 57.083 36.000 0.00 0.00 0.00 2.15
1182 1199 8.398665 TGATCGAGACGTAGATTAATGGATATG 58.601 37.037 0.00 0.00 0.00 1.78
1191 1208 3.246936 CGGTGTGATCGAGACGTAGATTA 59.753 47.826 0.00 0.00 0.00 1.75
1192 1209 2.031807 CGGTGTGATCGAGACGTAGATT 59.968 50.000 0.00 0.00 0.00 2.40
1205 1222 2.202743 CGTCGGCATCGGTGTGAT 60.203 61.111 0.00 0.00 38.01 3.06
1273 1290 3.610040 TTCGTTGCTGTATGATGTCCT 57.390 42.857 0.00 0.00 0.00 3.85
1300 1317 4.679662 TCTGTTACTCTAAAGGCGCATAC 58.320 43.478 10.83 0.00 0.00 2.39
1311 1328 4.030913 CCCATGGTCCTTCTGTTACTCTA 58.969 47.826 11.73 0.00 0.00 2.43
1329 1346 1.227853 GATTACGCCGAAGCCCCAT 60.228 57.895 0.00 0.00 34.57 4.00
1368 1385 4.081420 ACATCATCCCTCAAGTACACAGAC 60.081 45.833 0.00 0.00 0.00 3.51
1467 1487 1.301716 GTGGTGCATGTCTGACGGT 60.302 57.895 2.98 0.00 0.00 4.83
1614 1634 1.944430 GCGGTCTTTTCCTTCATCGGT 60.944 52.381 0.00 0.00 0.00 4.69
1642 1662 5.187381 TGGCATCCATGTTGTTGATTTGTAT 59.813 36.000 0.00 0.00 0.00 2.29
1654 1674 2.964464 TGAACACTTTGGCATCCATGTT 59.036 40.909 6.63 6.63 37.08 2.71
1677 1697 0.990374 AGATGAAGTGGAGCAAGGCT 59.010 50.000 0.00 0.00 43.88 4.58
1725 1745 4.430765 ATCACCGTCGCGTCACCC 62.431 66.667 5.77 0.00 0.00 4.61
1732 1752 2.887568 CTGAGCCATCACCGTCGC 60.888 66.667 0.00 0.00 0.00 5.19
1739 1759 4.553668 GCTGATGCTGAGCCATCA 57.446 55.556 15.28 15.28 46.78 3.07
1788 1808 2.948979 CTCCTCGTAGATCAGCTTGAGT 59.051 50.000 0.00 0.00 33.89 3.41
1802 1822 2.601666 TGCAGTGCCTCTCCTCGT 60.602 61.111 13.72 0.00 0.00 4.18
1848 1868 1.674322 CTCGGCCAATCCCAACGTT 60.674 57.895 2.24 0.00 0.00 3.99
1856 1876 2.719979 CATGCTGCTCGGCCAATC 59.280 61.111 2.24 0.00 0.00 2.67
1872 1892 2.124529 TTGAGCGCACCACAACCA 60.125 55.556 11.47 0.00 0.00 3.67
1878 1898 2.669569 GCCTTCTTGAGCGCACCA 60.670 61.111 11.47 3.86 0.00 4.17
1896 1916 2.171870 AGAAGTGAGGAACCCGAAACAA 59.828 45.455 0.00 0.00 0.00 2.83
1899 1919 1.346722 GGAGAAGTGAGGAACCCGAAA 59.653 52.381 0.00 0.00 0.00 3.46
1903 1923 1.597461 CCGGAGAAGTGAGGAACCC 59.403 63.158 0.00 0.00 0.00 4.11
1984 2004 1.531578 GCCAACAAACTCCTCGAGAAC 59.468 52.381 15.71 0.00 33.32 3.01
2133 2153 2.649034 GAGGTCTTGCGTCGTCCA 59.351 61.111 0.00 0.00 0.00 4.02
2188 2208 1.811778 TGCCCTGCCTTGATATCTCT 58.188 50.000 3.98 0.00 0.00 3.10
2225 2245 2.133553 GATCATCATGGCTCACGTCAG 58.866 52.381 0.00 0.00 0.00 3.51
2281 2301 4.568592 CCTCCTTAGCACCAAAGAGGAAAT 60.569 45.833 0.00 0.00 41.22 2.17
2372 2392 2.050350 CCGTCTTGCCGTCCTCCTA 61.050 63.158 0.00 0.00 0.00 2.94
2414 2434 2.338500 GAAAAGCTCTAGTGGTGACGG 58.662 52.381 0.00 0.00 0.00 4.79
2444 2464 5.221843 ACAAGCTATCCTGACAAAAGTGGTA 60.222 40.000 0.00 0.00 0.00 3.25
2496 2516 1.228154 GAAGGGAGCCAACAACGGT 60.228 57.895 0.00 0.00 0.00 4.83
2591 2613 2.484264 GTGCTAGTGTTGGCTTTCGATT 59.516 45.455 0.00 0.00 0.00 3.34
2890 2913 4.992982 TGGCACCCCTACCTGGCA 62.993 66.667 0.00 0.00 40.40 4.92
2915 2938 5.514274 AAATGTCACGGATGTGTCTTTTT 57.486 34.783 0.00 0.00 46.49 1.94
2916 2939 5.280945 CAAAATGTCACGGATGTGTCTTTT 58.719 37.500 0.00 0.00 46.49 2.27
2917 2940 4.261572 CCAAAATGTCACGGATGTGTCTTT 60.262 41.667 0.00 0.00 46.49 2.52
2918 2941 3.253188 CCAAAATGTCACGGATGTGTCTT 59.747 43.478 0.00 0.00 46.49 3.01
2919 2942 2.813754 CCAAAATGTCACGGATGTGTCT 59.186 45.455 0.00 0.00 46.49 3.41
2920 2943 2.095263 CCCAAAATGTCACGGATGTGTC 60.095 50.000 0.00 0.00 46.49 3.67
2921 2944 1.885887 CCCAAAATGTCACGGATGTGT 59.114 47.619 0.00 0.00 46.49 3.72
2923 2946 0.887933 GCCCAAAATGTCACGGATGT 59.112 50.000 0.00 0.00 0.00 3.06
2924 2947 0.173255 GGCCCAAAATGTCACGGATG 59.827 55.000 0.00 0.00 0.00 3.51
2925 2948 1.312371 CGGCCCAAAATGTCACGGAT 61.312 55.000 0.00 0.00 0.00 4.18
2926 2949 1.969064 CGGCCCAAAATGTCACGGA 60.969 57.895 0.00 0.00 0.00 4.69
2927 2950 1.519751 TTCGGCCCAAAATGTCACGG 61.520 55.000 0.00 0.00 0.00 4.94
2928 2951 0.386731 GTTCGGCCCAAAATGTCACG 60.387 55.000 0.00 0.00 0.00 4.35
2929 2952 0.386731 CGTTCGGCCCAAAATGTCAC 60.387 55.000 0.00 0.00 0.00 3.67
2930 2953 0.535328 TCGTTCGGCCCAAAATGTCA 60.535 50.000 0.00 0.00 0.00 3.58
2931 2954 0.594110 TTCGTTCGGCCCAAAATGTC 59.406 50.000 0.00 0.00 0.00 3.06
2932 2955 1.253100 ATTCGTTCGGCCCAAAATGT 58.747 45.000 0.00 0.00 0.00 2.71
2933 2956 2.362169 AATTCGTTCGGCCCAAAATG 57.638 45.000 0.00 0.00 0.00 2.32
2934 2957 3.394674 AAAATTCGTTCGGCCCAAAAT 57.605 38.095 0.00 0.00 0.00 1.82
2935 2958 2.892784 AAAATTCGTTCGGCCCAAAA 57.107 40.000 0.00 0.00 0.00 2.44
2936 2959 2.892784 AAAAATTCGTTCGGCCCAAA 57.107 40.000 0.00 0.00 0.00 3.28
2962 2985 6.542370 TCGTCATAGAAGTGTCATCTGTATGA 59.458 38.462 0.00 0.00 39.87 2.15
2963 2986 6.729187 TCGTCATAGAAGTGTCATCTGTATG 58.271 40.000 0.00 0.00 0.00 2.39
2964 2987 6.944234 TCGTCATAGAAGTGTCATCTGTAT 57.056 37.500 0.00 0.00 0.00 2.29
2965 2988 6.944234 ATCGTCATAGAAGTGTCATCTGTA 57.056 37.500 0.00 0.00 0.00 2.74
2966 2989 5.843673 ATCGTCATAGAAGTGTCATCTGT 57.156 39.130 0.00 0.00 0.00 3.41
2967 2990 8.697960 CAATTATCGTCATAGAAGTGTCATCTG 58.302 37.037 0.00 0.00 0.00 2.90
2968 2991 8.417106 ACAATTATCGTCATAGAAGTGTCATCT 58.583 33.333 0.00 0.00 0.00 2.90
2969 2992 8.483218 CACAATTATCGTCATAGAAGTGTCATC 58.517 37.037 0.00 0.00 0.00 2.92
2970 2993 8.197439 TCACAATTATCGTCATAGAAGTGTCAT 58.803 33.333 0.00 0.00 0.00 3.06
2971 2994 7.488150 GTCACAATTATCGTCATAGAAGTGTCA 59.512 37.037 0.00 0.00 0.00 3.58
2972 2995 7.488150 TGTCACAATTATCGTCATAGAAGTGTC 59.512 37.037 0.00 0.00 0.00 3.67
2973 2996 7.320399 TGTCACAATTATCGTCATAGAAGTGT 58.680 34.615 0.00 0.00 0.00 3.55
2974 2997 7.755582 TGTCACAATTATCGTCATAGAAGTG 57.244 36.000 0.00 0.00 0.00 3.16
2975 2998 8.771920 TTTGTCACAATTATCGTCATAGAAGT 57.228 30.769 0.00 0.00 0.00 3.01
2976 2999 9.478019 GTTTTGTCACAATTATCGTCATAGAAG 57.522 33.333 0.00 0.00 0.00 2.85
2977 3000 8.447833 GGTTTTGTCACAATTATCGTCATAGAA 58.552 33.333 0.00 0.00 0.00 2.10
2978 3001 7.065324 GGGTTTTGTCACAATTATCGTCATAGA 59.935 37.037 0.00 0.00 0.00 1.98
2979 3002 7.186804 GGGTTTTGTCACAATTATCGTCATAG 58.813 38.462 0.00 0.00 0.00 2.23
2980 3003 6.183360 CGGGTTTTGTCACAATTATCGTCATA 60.183 38.462 0.00 0.00 0.00 2.15
2981 3004 5.391523 CGGGTTTTGTCACAATTATCGTCAT 60.392 40.000 0.00 0.00 0.00 3.06
2982 3005 4.083749 CGGGTTTTGTCACAATTATCGTCA 60.084 41.667 0.00 0.00 0.00 4.35
2983 3006 4.399978 CGGGTTTTGTCACAATTATCGTC 58.600 43.478 0.00 0.00 0.00 4.20
2984 3007 3.189702 CCGGGTTTTGTCACAATTATCGT 59.810 43.478 0.00 0.00 0.00 3.73
2985 3008 3.189702 ACCGGGTTTTGTCACAATTATCG 59.810 43.478 6.32 0.00 0.00 2.92
2986 3009 4.776795 ACCGGGTTTTGTCACAATTATC 57.223 40.909 6.32 0.00 0.00 1.75
2987 3010 5.946972 TGATACCGGGTTTTGTCACAATTAT 59.053 36.000 4.31 0.00 0.00 1.28
2988 3011 5.314529 TGATACCGGGTTTTGTCACAATTA 58.685 37.500 4.31 0.00 0.00 1.40
2989 3012 4.145807 TGATACCGGGTTTTGTCACAATT 58.854 39.130 4.31 0.00 0.00 2.32
2990 3013 3.757270 TGATACCGGGTTTTGTCACAAT 58.243 40.909 4.31 0.00 0.00 2.71
2991 3014 3.210232 TGATACCGGGTTTTGTCACAA 57.790 42.857 4.31 0.00 0.00 3.33
2992 3015 2.932855 TGATACCGGGTTTTGTCACA 57.067 45.000 4.31 0.00 0.00 3.58
2993 3016 3.340034 TGATGATACCGGGTTTTGTCAC 58.660 45.455 4.31 2.17 0.00 3.67
2994 3017 3.704800 TGATGATACCGGGTTTTGTCA 57.295 42.857 4.31 5.88 0.00 3.58
2995 3018 5.607477 TCTATGATGATACCGGGTTTTGTC 58.393 41.667 4.31 0.82 0.00 3.18
2996 3019 5.623956 TCTATGATGATACCGGGTTTTGT 57.376 39.130 4.31 0.00 0.00 2.83
2997 3020 5.997746 ACATCTATGATGATACCGGGTTTTG 59.002 40.000 4.31 0.00 0.00 2.44
2998 3021 5.997746 CACATCTATGATGATACCGGGTTTT 59.002 40.000 4.31 0.00 0.00 2.43
2999 3022 5.513094 CCACATCTATGATGATACCGGGTTT 60.513 44.000 4.31 0.00 0.00 3.27
3000 3023 4.020218 CCACATCTATGATGATACCGGGTT 60.020 45.833 4.31 0.00 0.00 4.11
3001 3024 3.515502 CCACATCTATGATGATACCGGGT 59.484 47.826 6.32 4.46 0.00 5.28
3002 3025 3.515502 ACCACATCTATGATGATACCGGG 59.484 47.826 6.32 0.00 0.00 5.73
3003 3026 4.498241 CACCACATCTATGATGATACCGG 58.502 47.826 13.63 0.00 0.00 5.28
3004 3027 4.498241 CCACCACATCTATGATGATACCG 58.502 47.826 13.63 0.06 0.00 4.02
3005 3028 4.836825 CCCACCACATCTATGATGATACC 58.163 47.826 13.63 0.00 0.00 2.73
3006 3029 4.019860 AGCCCACCACATCTATGATGATAC 60.020 45.833 13.63 0.00 0.00 2.24
3007 3030 4.170449 AGCCCACCACATCTATGATGATA 58.830 43.478 13.63 0.00 0.00 2.15
3008 3031 2.984604 AGCCCACCACATCTATGATGAT 59.015 45.455 13.63 0.00 0.00 2.45
3009 3032 2.369860 GAGCCCACCACATCTATGATGA 59.630 50.000 13.63 0.00 0.00 2.92
3010 3033 2.551721 GGAGCCCACCACATCTATGATG 60.552 54.545 6.06 6.06 0.00 3.07
3011 3034 1.701847 GGAGCCCACCACATCTATGAT 59.298 52.381 0.00 0.00 0.00 2.45
3012 3035 1.131638 GGAGCCCACCACATCTATGA 58.868 55.000 0.00 0.00 0.00 2.15
3013 3036 1.135094 AGGAGCCCACCACATCTATG 58.865 55.000 0.00 0.00 0.00 2.23
3014 3037 2.090494 AGTAGGAGCCCACCACATCTAT 60.090 50.000 0.00 0.00 0.00 1.98
3015 3038 1.291033 AGTAGGAGCCCACCACATCTA 59.709 52.381 0.00 0.00 0.00 1.98
3016 3039 0.043334 AGTAGGAGCCCACCACATCT 59.957 55.000 0.00 0.00 0.00 2.90
3017 3040 0.912486 AAGTAGGAGCCCACCACATC 59.088 55.000 0.00 0.00 0.00 3.06
3018 3041 0.912486 GAAGTAGGAGCCCACCACAT 59.088 55.000 0.00 0.00 0.00 3.21
3019 3042 0.178903 AGAAGTAGGAGCCCACCACA 60.179 55.000 0.00 0.00 0.00 4.17
3020 3043 1.861982 TAGAAGTAGGAGCCCACCAC 58.138 55.000 0.00 0.00 0.00 4.16
3021 3044 2.023404 TCATAGAAGTAGGAGCCCACCA 60.023 50.000 0.00 0.00 0.00 4.17
3022 3045 2.365941 GTCATAGAAGTAGGAGCCCACC 59.634 54.545 0.00 0.00 0.00 4.61
3023 3046 3.031736 TGTCATAGAAGTAGGAGCCCAC 58.968 50.000 0.00 0.00 0.00 4.61
3024 3047 3.398318 TGTCATAGAAGTAGGAGCCCA 57.602 47.619 0.00 0.00 0.00 5.36
3025 3048 4.755266 TTTGTCATAGAAGTAGGAGCCC 57.245 45.455 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.