Multiple sequence alignment - TraesCS4A01G409200

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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 TraesCS4A01G409200 chr4A 100.000 3170 0 0 1 3170 681789012 681792181 0.000000e+00 5854.0
1 TraesCS4A01G409200 chr4D 90.865 1248 47 20 1561 2778 474377599 474376389 0.000000e+00 1611.0
2 TraesCS4A01G409200 chr4D 91.385 859 57 3 4 846 389486172 389485315 0.000000e+00 1160.0
3 TraesCS4A01G409200 chr4D 90.128 861 69 3 1 846 49296347 49297206 0.000000e+00 1105.0
4 TraesCS4A01G409200 chr4D 91.535 697 28 9 850 1517 474378297 474377603 0.000000e+00 931.0
5 TraesCS4A01G409200 chr4D 96.262 214 8 0 2925 3138 474376398 474376185 5.030000e-93 351.0
6 TraesCS4A01G409200 chr4D 90.968 155 7 2 2778 2926 308485262 308485415 5.360000e-48 202.0
7 TraesCS4A01G409200 chr4B 89.936 1242 50 20 1566 2778 597741962 597740767 0.000000e+00 1531.0
8 TraesCS4A01G409200 chr4B 93.125 640 21 7 897 1517 597742614 597741979 0.000000e+00 917.0
9 TraesCS4A01G409200 chr4B 94.170 223 13 0 2925 3147 597740776 597740554 1.090000e-89 340.0
10 TraesCS4A01G409200 chr4B 92.617 149 7 3 2778 2926 382658063 382658207 8.910000e-51 211.0
11 TraesCS4A01G409200 chr2D 92.424 858 50 3 4 846 364969671 364968814 0.000000e+00 1210.0
12 TraesCS4A01G409200 chr2D 91.425 863 56 4 4 850 20775794 20774934 0.000000e+00 1168.0
13 TraesCS4A01G409200 chr2D 90.592 861 65 6 1 846 513913513 513914372 0.000000e+00 1127.0
14 TraesCS4A01G409200 chr2D 79.905 1050 132 44 1095 2101 373903441 373902428 0.000000e+00 697.0
15 TraesCS4A01G409200 chr2D 81.132 106 11 6 2826 2926 192854286 192854387 3.390000e-10 76.8
16 TraesCS4A01G409200 chr5D 91.379 870 60 1 1 855 521151196 521152065 0.000000e+00 1177.0
17 TraesCS4A01G409200 chr5D 91.067 862 61 2 1 847 558577595 558578455 0.000000e+00 1151.0
18 TraesCS4A01G409200 chr5D 89.382 857 72 9 7 847 439412453 439411600 0.000000e+00 1061.0
19 TraesCS4A01G409200 chr3D 93.130 786 39 1 76 846 283323295 283322510 0.000000e+00 1138.0
20 TraesCS4A01G409200 chr3D 90.093 858 69 8 4 846 496142013 496141157 0.000000e+00 1099.0
21 TraesCS4A01G409200 chr3D 91.092 797 54 4 4 785 531429807 531429013 0.000000e+00 1062.0
22 TraesCS4A01G409200 chr3D 88.394 853 75 13 2 847 262829813 262828978 0.000000e+00 1005.0
23 TraesCS4A01G409200 chr3D 87.779 851 83 13 1 847 212254132 212254965 0.000000e+00 976.0
24 TraesCS4A01G409200 chr6D 90.300 866 63 5 4 854 293051738 293050879 0.000000e+00 1114.0
25 TraesCS4A01G409200 chr1B 84.109 774 110 10 1 769 499651055 499650290 0.000000e+00 736.0
26 TraesCS4A01G409200 chr1B 86.486 148 11 3 2778 2924 29490556 29490417 1.520000e-33 154.0
27 TraesCS4A01G409200 chr2B 80.151 1058 125 47 1095 2101 443825235 443824212 0.000000e+00 712.0
28 TraesCS4A01G409200 chr2B 87.500 72 9 0 996 1067 443825382 443825311 2.030000e-12 84.2
29 TraesCS4A01G409200 chrUn 80.114 1051 129 49 1095 2101 300432729 300431715 0.000000e+00 710.0
30 TraesCS4A01G409200 chrUn 88.060 67 8 0 1001 1067 300432870 300432804 2.620000e-11 80.5
31 TraesCS4A01G409200 chr7B 95.302 149 7 0 2778 2926 713433090 713433238 1.470000e-58 237.0
32 TraesCS4A01G409200 chr7B 91.216 148 13 0 2779 2926 677713819 677713966 5.360000e-48 202.0
33 TraesCS4A01G409200 chr7B 96.970 33 1 0 2897 2929 718431406 718431438 4.420000e-04 56.5
34 TraesCS4A01G409200 chr5B 90.909 88 8 0 2779 2866 34902674 34902761 5.550000e-23 119.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G409200 chr4A 681789012 681792181 3169 False 5854.000000 5854 100.000000 1 3170 1 chr4A.!!$F1 3169
1 TraesCS4A01G409200 chr4D 389485315 389486172 857 True 1160.000000 1160 91.385000 4 846 1 chr4D.!!$R1 842
2 TraesCS4A01G409200 chr4D 49296347 49297206 859 False 1105.000000 1105 90.128000 1 846 1 chr4D.!!$F1 845
3 TraesCS4A01G409200 chr4D 474376185 474378297 2112 True 964.333333 1611 92.887333 850 3138 3 chr4D.!!$R2 2288
4 TraesCS4A01G409200 chr4B 597740554 597742614 2060 True 929.333333 1531 92.410333 897 3147 3 chr4B.!!$R1 2250
5 TraesCS4A01G409200 chr2D 364968814 364969671 857 True 1210.000000 1210 92.424000 4 846 1 chr2D.!!$R2 842
6 TraesCS4A01G409200 chr2D 20774934 20775794 860 True 1168.000000 1168 91.425000 4 850 1 chr2D.!!$R1 846
7 TraesCS4A01G409200 chr2D 513913513 513914372 859 False 1127.000000 1127 90.592000 1 846 1 chr2D.!!$F2 845
8 TraesCS4A01G409200 chr2D 373902428 373903441 1013 True 697.000000 697 79.905000 1095 2101 1 chr2D.!!$R3 1006
9 TraesCS4A01G409200 chr5D 521151196 521152065 869 False 1177.000000 1177 91.379000 1 855 1 chr5D.!!$F1 854
10 TraesCS4A01G409200 chr5D 558577595 558578455 860 False 1151.000000 1151 91.067000 1 847 1 chr5D.!!$F2 846
11 TraesCS4A01G409200 chr5D 439411600 439412453 853 True 1061.000000 1061 89.382000 7 847 1 chr5D.!!$R1 840
12 TraesCS4A01G409200 chr3D 283322510 283323295 785 True 1138.000000 1138 93.130000 76 846 1 chr3D.!!$R2 770
13 TraesCS4A01G409200 chr3D 496141157 496142013 856 True 1099.000000 1099 90.093000 4 846 1 chr3D.!!$R3 842
14 TraesCS4A01G409200 chr3D 531429013 531429807 794 True 1062.000000 1062 91.092000 4 785 1 chr3D.!!$R4 781
15 TraesCS4A01G409200 chr3D 262828978 262829813 835 True 1005.000000 1005 88.394000 2 847 1 chr3D.!!$R1 845
16 TraesCS4A01G409200 chr3D 212254132 212254965 833 False 976.000000 976 87.779000 1 847 1 chr3D.!!$F1 846
17 TraesCS4A01G409200 chr6D 293050879 293051738 859 True 1114.000000 1114 90.300000 4 854 1 chr6D.!!$R1 850
18 TraesCS4A01G409200 chr1B 499650290 499651055 765 True 736.000000 736 84.109000 1 769 1 chr1B.!!$R2 768
19 TraesCS4A01G409200 chr2B 443824212 443825382 1170 True 398.100000 712 83.825500 996 2101 2 chr2B.!!$R1 1105
20 TraesCS4A01G409200 chrUn 300431715 300432870 1155 True 395.250000 710 84.087000 1001 2101 2 chrUn.!!$R1 1100

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
445 463 0.826715 TGCGAGGAAGCAAGCTCTAT 59.173 50.0 0.0 0.0 45.06 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 2489 0.031178 GTCCCAGTGAACACGTACGT 59.969 55.0 16.72 16.72 36.2 3.57 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
258 261 5.239306 CAGTTGTGCTCTTGGATTTGACTAA 59.761 40.000 0.00 0.00 0.00 2.24
318 321 5.306678 TGCAAGTTTTGGTATTGGGAAGAAT 59.693 36.000 0.00 0.00 0.00 2.40
445 463 0.826715 TGCGAGGAAGCAAGCTCTAT 59.173 50.000 0.00 0.00 45.06 1.98
497 518 1.198713 ACATCGAGCCTTCTCCACAT 58.801 50.000 0.00 0.00 35.94 3.21
643 665 5.857471 ATTTGGTGATGTATTCCCATGTG 57.143 39.130 0.00 0.00 0.00 3.21
785 808 2.375345 CGACCCCATTGCCCTACCT 61.375 63.158 0.00 0.00 0.00 3.08
859 882 1.693799 TGGCCTTTAGGAGGGGATTT 58.306 50.000 3.32 0.00 46.40 2.17
870 893 2.091830 GGAGGGGATTTGGAGGTAAAGG 60.092 54.545 0.00 0.00 0.00 3.11
878 902 3.412237 TTGGAGGTAAAGGTTTCTCCG 57.588 47.619 0.00 0.00 46.42 4.63
884 908 6.183360 TGGAGGTAAAGGTTTCTCCGTATATG 60.183 42.308 0.00 0.00 46.42 1.78
943 973 6.489022 GCCTTTGGGAGTTATAACCGATTAAT 59.511 38.462 12.05 0.00 33.58 1.40
999 1043 2.248431 GCTTCGACCGTTGCACAC 59.752 61.111 0.00 0.00 0.00 3.82
1070 1114 2.921221 AGAGTTCCCCATTCCTCAAGA 58.079 47.619 0.00 0.00 0.00 3.02
1093 1146 4.527038 ACTTGGTGCTTCTACTACTAGCAA 59.473 41.667 0.00 0.00 45.54 3.91
1198 1305 4.382254 GGTGAATATGACGGTGACCTACAA 60.382 45.833 0.00 0.00 0.00 2.41
1343 1455 3.869473 TTGGCCACCTGACGCGTAC 62.869 63.158 13.97 6.75 0.00 3.67
1344 1456 4.367023 GGCCACCTGACGCGTACA 62.367 66.667 13.97 11.56 0.00 2.90
1434 1547 2.203266 GATGTGCCAGGGCCTAGC 60.203 66.667 17.62 17.62 41.09 3.42
1491 1613 3.767673 TGTACTAACCCAACCTAGCTCAG 59.232 47.826 0.00 0.00 0.00 3.35
1507 1629 2.100584 GCTCAGTCGATCAGAAGTCCAT 59.899 50.000 0.00 0.00 0.00 3.41
1520 1646 5.306937 TCAGAAGTCCATCCAGTACAAAGAA 59.693 40.000 0.00 0.00 0.00 2.52
1521 1647 5.997746 CAGAAGTCCATCCAGTACAAAGAAA 59.002 40.000 0.00 0.00 0.00 2.52
1522 1648 6.656693 CAGAAGTCCATCCAGTACAAAGAAAT 59.343 38.462 0.00 0.00 0.00 2.17
1574 1708 6.535963 TCTCATGAGCCATGTATATCGAAT 57.464 37.500 18.36 0.00 41.98 3.34
1592 1726 3.438087 CGAATTGCTCAGTCCAAGTGATT 59.562 43.478 0.00 0.00 0.00 2.57
1616 1760 7.701539 TGAGCACAAATTAATTATCTGGTGT 57.298 32.000 0.01 0.00 0.00 4.16
1626 1770 8.924511 ATTAATTATCTGGTGTCCCATTAGTG 57.075 34.615 0.00 0.00 40.90 2.74
1804 1951 0.961753 CTTCTTTTGGTCAGTGCCCC 59.038 55.000 0.00 0.00 0.00 5.80
1806 1953 0.555769 TCTTTTGGTCAGTGCCCCTT 59.444 50.000 0.00 0.00 0.00 3.95
1807 1954 1.063266 TCTTTTGGTCAGTGCCCCTTT 60.063 47.619 0.00 0.00 0.00 3.11
1809 1956 1.872773 TTTGGTCAGTGCCCCTTTTT 58.127 45.000 0.00 0.00 0.00 1.94
1811 1958 0.555769 TGGTCAGTGCCCCTTTTTCT 59.444 50.000 0.00 0.00 0.00 2.52
1812 1959 0.961753 GGTCAGTGCCCCTTTTTCTG 59.038 55.000 0.00 0.00 0.00 3.02
1813 1960 1.478654 GGTCAGTGCCCCTTTTTCTGA 60.479 52.381 0.00 0.00 33.60 3.27
1814 1961 2.519013 GTCAGTGCCCCTTTTTCTGAT 58.481 47.619 0.00 0.00 37.46 2.90
1818 1982 2.893489 AGTGCCCCTTTTTCTGATTGAC 59.107 45.455 0.00 0.00 0.00 3.18
1821 1985 3.157087 GCCCCTTTTTCTGATTGACTGA 58.843 45.455 0.00 0.00 0.00 3.41
1833 1997 7.904558 TCTGATTGACTGACTACATCCTTAT 57.095 36.000 0.00 0.00 0.00 1.73
1834 1998 8.311395 TCTGATTGACTGACTACATCCTTATT 57.689 34.615 0.00 0.00 0.00 1.40
1889 2059 1.136984 CGAGGTGGTGAGCTACGAC 59.863 63.158 0.00 0.00 37.29 4.34
2103 2273 1.669502 GCCGCTGATGTGAAAAATGCA 60.670 47.619 0.00 0.00 0.00 3.96
2112 2282 3.456280 TGTGAAAAATGCAACAAGCCTC 58.544 40.909 0.00 0.00 44.83 4.70
2183 2353 5.607119 TCCGTTCAAATAAGAGTTTGCTC 57.393 39.130 0.00 0.00 38.61 4.26
2224 2394 5.243283 TGTTTCTGGTAGTCTTCCTACTGTC 59.757 44.000 0.00 0.00 44.66 3.51
2227 2397 3.428532 TGGTAGTCTTCCTACTGTCCAC 58.571 50.000 0.00 0.00 44.66 4.02
2228 2398 3.075582 TGGTAGTCTTCCTACTGTCCACT 59.924 47.826 0.00 0.00 44.66 4.00
2303 2492 8.891671 TTTAGTTCAACTCCTATTTTGTACGT 57.108 30.769 0.00 0.00 30.67 3.57
2343 2536 2.902486 TGGGAGCAGAATGATAGCTAGG 59.098 50.000 0.00 0.00 39.69 3.02
2403 2598 0.178924 AGGTGGAAAAGGCAATGGCT 60.179 50.000 2.53 2.53 41.24 4.75
2468 2663 6.017357 GGCCTATAATCTTTCTTACCCGTTTG 60.017 42.308 0.00 0.00 0.00 2.93
2575 2774 5.471116 TGTCTTGGTTGATCTTGATTGTCTG 59.529 40.000 0.00 0.00 0.00 3.51
2576 2775 5.702670 GTCTTGGTTGATCTTGATTGTCTGA 59.297 40.000 0.00 0.00 0.00 3.27
2577 2776 6.373774 GTCTTGGTTGATCTTGATTGTCTGAT 59.626 38.462 0.00 0.00 0.00 2.90
2578 2777 6.373495 TCTTGGTTGATCTTGATTGTCTGATG 59.627 38.462 0.00 0.00 0.00 3.07
2579 2778 5.807909 TGGTTGATCTTGATTGTCTGATGA 58.192 37.500 0.00 0.00 0.00 2.92
2580 2779 5.878669 TGGTTGATCTTGATTGTCTGATGAG 59.121 40.000 0.00 0.00 0.00 2.90
2581 2780 5.879223 GGTTGATCTTGATTGTCTGATGAGT 59.121 40.000 0.00 0.00 0.00 3.41
2582 2781 7.044181 GGTTGATCTTGATTGTCTGATGAGTA 58.956 38.462 0.00 0.00 0.00 2.59
2583 2782 7.010923 GGTTGATCTTGATTGTCTGATGAGTAC 59.989 40.741 0.00 0.00 0.00 2.73
2584 2783 6.268566 TGATCTTGATTGTCTGATGAGTACG 58.731 40.000 0.00 0.00 0.00 3.67
2626 2825 1.202592 TGCCGTATCTGTTGTGTGTGT 60.203 47.619 0.00 0.00 0.00 3.72
2627 2826 1.194547 GCCGTATCTGTTGTGTGTGTG 59.805 52.381 0.00 0.00 0.00 3.82
2696 2895 1.000396 AGGCATCAGTTCTTGGCCC 60.000 57.895 0.00 0.00 45.72 5.80
2795 2994 4.451150 CAGTAGCGGCGGCAGGAA 62.451 66.667 19.21 0.00 43.41 3.36
2796 2995 3.702048 AGTAGCGGCGGCAGGAAA 61.702 61.111 19.21 0.00 43.41 3.13
2797 2996 2.744709 GTAGCGGCGGCAGGAAAA 60.745 61.111 19.21 0.00 43.41 2.29
2798 2997 2.032834 TAGCGGCGGCAGGAAAAA 59.967 55.556 19.21 0.00 43.41 1.94
2799 2998 2.038269 TAGCGGCGGCAGGAAAAAG 61.038 57.895 19.21 0.00 43.41 2.27
2800 2999 4.419939 GCGGCGGCAGGAAAAAGG 62.420 66.667 9.78 0.00 39.62 3.11
2801 3000 2.671619 CGGCGGCAGGAAAAAGGA 60.672 61.111 10.53 0.00 0.00 3.36
2802 3001 2.265182 CGGCGGCAGGAAAAAGGAA 61.265 57.895 10.53 0.00 0.00 3.36
2803 3002 1.289066 GGCGGCAGGAAAAAGGAAC 59.711 57.895 3.07 0.00 0.00 3.62
2804 3003 1.081442 GCGGCAGGAAAAAGGAACG 60.081 57.895 0.00 0.00 0.00 3.95
2805 3004 1.081442 CGGCAGGAAAAAGGAACGC 60.081 57.895 0.00 0.00 0.00 4.84
2806 3005 1.289066 GGCAGGAAAAAGGAACGCC 59.711 57.895 0.00 0.00 0.00 5.68
2807 3006 1.289066 GCAGGAAAAAGGAACGCCC 59.711 57.895 0.00 0.00 33.31 6.13
2808 3007 1.964448 CAGGAAAAAGGAACGCCCC 59.036 57.895 0.00 0.00 34.66 5.80
2809 3008 0.825840 CAGGAAAAAGGAACGCCCCA 60.826 55.000 0.00 0.00 34.66 4.96
2810 3009 0.539669 AGGAAAAAGGAACGCCCCAG 60.540 55.000 0.00 0.00 34.66 4.45
2811 3010 1.532604 GGAAAAAGGAACGCCCCAGG 61.533 60.000 0.00 0.00 34.66 4.45
2812 3011 2.154798 GAAAAAGGAACGCCCCAGGC 62.155 60.000 0.00 0.00 46.75 4.85
2825 3024 3.333219 CAGGCAGCCTCCAGGGAA 61.333 66.667 12.53 0.00 37.23 3.97
2826 3025 3.334054 AGGCAGCCTCCAGGGAAC 61.334 66.667 8.70 0.00 37.23 3.62
2827 3026 3.334054 GGCAGCCTCCAGGGAACT 61.334 66.667 3.29 0.00 46.44 3.01
2840 3039 1.550976 AGGGAACTGTAGCACTGTAGC 59.449 52.381 0.00 0.00 41.13 3.58
2841 3040 2.823535 AGGGAACTGTAGCACTGTAGCT 60.824 50.000 9.15 9.15 44.20 3.32
2842 3041 2.758979 GGGAACTGTAGCACTGTAGCTA 59.241 50.000 7.54 7.54 44.50 3.32
2859 3058 3.786635 AGCTACAGTACTGCTACAATGC 58.213 45.455 22.90 14.84 35.05 3.56
2860 3059 2.866762 GCTACAGTACTGCTACAATGCC 59.133 50.000 22.90 0.00 0.00 4.40
2861 3060 2.403252 ACAGTACTGCTACAATGCCC 57.597 50.000 22.90 0.00 0.00 5.36
2862 3061 1.628340 ACAGTACTGCTACAATGCCCA 59.372 47.619 22.90 0.00 0.00 5.36
2863 3062 2.039746 ACAGTACTGCTACAATGCCCAA 59.960 45.455 22.90 0.00 0.00 4.12
2864 3063 3.081061 CAGTACTGCTACAATGCCCAAA 58.919 45.455 10.54 0.00 0.00 3.28
2865 3064 3.127548 CAGTACTGCTACAATGCCCAAAG 59.872 47.826 10.54 0.00 0.00 2.77
2866 3065 2.584835 ACTGCTACAATGCCCAAAGA 57.415 45.000 0.00 0.00 0.00 2.52
2867 3066 2.875296 ACTGCTACAATGCCCAAAGAA 58.125 42.857 0.00 0.00 0.00 2.52
2868 3067 3.230134 ACTGCTACAATGCCCAAAGAAA 58.770 40.909 0.00 0.00 0.00 2.52
2869 3068 3.640967 ACTGCTACAATGCCCAAAGAAAA 59.359 39.130 0.00 0.00 0.00 2.29
2870 3069 4.284234 ACTGCTACAATGCCCAAAGAAAAT 59.716 37.500 0.00 0.00 0.00 1.82
2871 3070 4.567971 TGCTACAATGCCCAAAGAAAATG 58.432 39.130 0.00 0.00 0.00 2.32
2872 3071 3.371898 GCTACAATGCCCAAAGAAAATGC 59.628 43.478 0.00 0.00 0.00 3.56
2873 3072 3.488778 ACAATGCCCAAAGAAAATGCA 57.511 38.095 0.00 0.00 36.23 3.96
2874 3073 4.023726 ACAATGCCCAAAGAAAATGCAT 57.976 36.364 0.00 0.00 44.02 3.96
2875 3074 4.004982 ACAATGCCCAAAGAAAATGCATC 58.995 39.130 0.00 0.00 41.49 3.91
2876 3075 4.258543 CAATGCCCAAAGAAAATGCATCT 58.741 39.130 0.00 0.00 41.49 2.90
2877 3076 3.598019 TGCCCAAAGAAAATGCATCTC 57.402 42.857 0.00 0.00 0.00 2.75
2878 3077 2.898612 TGCCCAAAGAAAATGCATCTCA 59.101 40.909 0.00 0.00 0.00 3.27
2879 3078 3.256558 GCCCAAAGAAAATGCATCTCAC 58.743 45.455 0.00 0.00 0.00 3.51
2880 3079 3.504863 CCCAAAGAAAATGCATCTCACG 58.495 45.455 0.00 0.00 0.00 4.35
2881 3080 2.919229 CCAAAGAAAATGCATCTCACGC 59.081 45.455 0.00 0.00 0.00 5.34
2882 3081 2.919229 CAAAGAAAATGCATCTCACGCC 59.081 45.455 0.00 0.00 0.00 5.68
2883 3082 1.098050 AGAAAATGCATCTCACGCCC 58.902 50.000 0.00 0.00 0.00 6.13
2884 3083 0.101219 GAAAATGCATCTCACGCCCC 59.899 55.000 0.00 0.00 0.00 5.80
2885 3084 0.611618 AAAATGCATCTCACGCCCCA 60.612 50.000 0.00 0.00 0.00 4.96
2886 3085 1.033746 AAATGCATCTCACGCCCCAG 61.034 55.000 0.00 0.00 0.00 4.45
2887 3086 2.898920 AATGCATCTCACGCCCCAGG 62.899 60.000 0.00 0.00 0.00 4.45
2925 3124 4.767255 GGCCTGTCTCCGCCACTG 62.767 72.222 0.00 0.00 45.01 3.66
2979 3178 1.955778 CACTTTCTGGGTCAACATGCA 59.044 47.619 0.00 0.00 0.00 3.96
3108 3307 7.759489 TGGCTAACTAAGACAATCAACAAAT 57.241 32.000 0.00 0.00 41.66 2.32
3119 3318 8.877864 AGACAATCAACAAATATGGAAGGTAA 57.122 30.769 0.00 0.00 0.00 2.85
3138 3337 8.907222 AAGGTAAAAGTAGTTTTAACGGATGA 57.093 30.769 20.12 0.00 46.46 2.92
3140 3339 8.996271 AGGTAAAAGTAGTTTTAACGGATGAAG 58.004 33.333 20.12 0.00 46.46 3.02
3144 3343 6.237313 AGTAGTTTTAACGGATGAAGCAAC 57.763 37.500 0.00 0.00 0.00 4.17
3147 3346 6.481954 AGTTTTAACGGATGAAGCAACTAG 57.518 37.500 0.00 0.00 0.00 2.57
3148 3347 4.939509 TTTAACGGATGAAGCAACTAGC 57.060 40.909 0.00 0.00 46.19 3.42
3156 3355 2.964740 TGAAGCAACTAGCAGCTAGTG 58.035 47.619 31.66 24.76 45.28 2.74
3164 3363 2.573869 GCAGCTAGTGCGACTCCA 59.426 61.111 0.00 0.00 43.99 3.86
3165 3364 1.807573 GCAGCTAGTGCGACTCCAC 60.808 63.158 0.00 0.00 43.99 4.02
3166 3365 1.153745 CAGCTAGTGCGACTCCACC 60.154 63.158 0.00 0.00 45.42 4.61
3167 3366 1.304547 AGCTAGTGCGACTCCACCT 60.305 57.895 0.00 0.00 45.42 4.00
3168 3367 0.034380 AGCTAGTGCGACTCCACCTA 60.034 55.000 0.00 0.00 45.42 3.08
3169 3368 1.033574 GCTAGTGCGACTCCACCTAT 58.966 55.000 0.00 0.00 36.38 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 0.321653 CTTTTGGGCTAGCACCGAGT 60.322 55.000 15.98 0.00 0.00 4.18
343 346 6.163476 AGTGCACGAACATCTACTAAATTGA 58.837 36.000 12.01 0.00 0.00 2.57
439 457 8.690680 TTTCTTCGAGTCTAAAGAAATAGAGC 57.309 34.615 18.82 0.00 43.17 4.09
479 497 3.006217 TGATATGTGGAGAAGGCTCGATG 59.994 47.826 0.00 0.00 42.25 3.84
497 518 6.017687 CCTTCTCGATGCATTCATTGTTGATA 60.018 38.462 0.00 0.00 35.89 2.15
584 605 7.462571 AACAAGACCAAGTAAAACAAGAACT 57.537 32.000 0.00 0.00 0.00 3.01
859 882 2.332117 ACGGAGAAACCTTTACCTCCA 58.668 47.619 0.00 0.00 44.03 3.86
870 893 4.377897 CCTCCCAACATATACGGAGAAAC 58.622 47.826 3.51 0.00 43.96 2.78
917 947 2.092807 TCGGTTATAACTCCCAAAGGCC 60.093 50.000 15.05 0.00 0.00 5.19
999 1043 4.705507 TGGCGTAGAGGCTCTATTTATAGG 59.294 45.833 25.93 12.03 46.88 2.57
1058 1102 1.815003 GCACCAAGTCTTGAGGAATGG 59.185 52.381 14.42 0.00 38.45 3.16
1070 1114 4.087182 TGCTAGTAGTAGAAGCACCAAGT 58.913 43.478 8.87 0.00 41.15 3.16
1115 1222 1.154073 GACGACGAGAGGGTTTCGG 60.154 63.158 0.00 0.00 42.12 4.30
1198 1305 1.367840 GACACCTGCTTGTCGGAGT 59.632 57.895 0.00 0.00 36.79 3.85
1343 1455 4.849111 GCTAGCTAGCTTACTTTGTGTG 57.151 45.455 33.71 0.56 45.62 3.82
1416 1529 2.512896 CTAGGCCCTGGCACATCC 59.487 66.667 10.86 0.00 44.11 3.51
1434 1547 0.605589 GCTCCCTCAGGTATGGATCG 59.394 60.000 0.00 0.00 0.00 3.69
1491 1613 2.428890 ACTGGATGGACTTCTGATCGAC 59.571 50.000 0.00 0.00 0.00 4.20
1548 1674 7.830099 TCGATATACATGGCTCATGAGATAT 57.170 36.000 27.04 17.44 43.81 1.63
1549 1675 7.645058 TTCGATATACATGGCTCATGAGATA 57.355 36.000 27.04 13.59 43.81 1.98
1550 1676 6.535963 TTCGATATACATGGCTCATGAGAT 57.464 37.500 27.04 11.80 43.81 2.75
1551 1677 5.982890 TTCGATATACATGGCTCATGAGA 57.017 39.130 27.04 6.75 43.81 3.27
1552 1678 6.456584 GCAATTCGATATACATGGCTCATGAG 60.457 42.308 18.84 18.84 43.81 2.90
1553 1679 5.352293 GCAATTCGATATACATGGCTCATGA 59.648 40.000 18.41 0.00 43.81 3.07
1554 1680 5.353400 AGCAATTCGATATACATGGCTCATG 59.647 40.000 12.06 12.06 46.18 3.07
1556 1682 4.898320 AGCAATTCGATATACATGGCTCA 58.102 39.130 0.00 0.00 0.00 4.26
1557 1683 4.931601 TGAGCAATTCGATATACATGGCTC 59.068 41.667 14.10 14.10 43.99 4.70
1558 1684 4.898320 TGAGCAATTCGATATACATGGCT 58.102 39.130 0.00 0.00 0.00 4.75
1559 1685 4.692625 ACTGAGCAATTCGATATACATGGC 59.307 41.667 0.00 0.00 0.00 4.40
1574 1708 3.405831 CTCAATCACTTGGACTGAGCAA 58.594 45.455 0.00 0.00 32.95 3.91
1592 1726 7.148086 GGACACCAGATAATTAATTTGTGCTCA 60.148 37.037 5.91 0.00 0.00 4.26
1616 1760 5.068254 CCCATAGGATAGCCACTAATGGGA 61.068 50.000 24.57 0.00 45.78 4.37
1626 1770 3.084786 GTTTGATGCCCATAGGATAGCC 58.915 50.000 0.00 0.00 33.47 3.93
1718 1865 7.137426 CACAAAAGCTCATAGCCTCATAATTC 58.863 38.462 0.00 0.00 43.77 2.17
1719 1866 6.604795 ACACAAAAGCTCATAGCCTCATAATT 59.395 34.615 0.00 0.00 43.77 1.40
1721 1868 5.500234 ACACAAAAGCTCATAGCCTCATAA 58.500 37.500 0.00 0.00 43.77 1.90
1722 1869 5.102953 ACACAAAAGCTCATAGCCTCATA 57.897 39.130 0.00 0.00 43.77 2.15
1723 1870 3.960571 ACACAAAAGCTCATAGCCTCAT 58.039 40.909 0.00 0.00 43.77 2.90
1804 1951 7.605691 AGGATGTAGTCAGTCAATCAGAAAAAG 59.394 37.037 0.00 0.00 0.00 2.27
1806 1953 7.009179 AGGATGTAGTCAGTCAATCAGAAAA 57.991 36.000 0.00 0.00 0.00 2.29
1807 1954 6.611613 AGGATGTAGTCAGTCAATCAGAAA 57.388 37.500 0.00 0.00 0.00 2.52
1809 1956 7.904558 ATAAGGATGTAGTCAGTCAATCAGA 57.095 36.000 0.00 0.00 0.00 3.27
1811 1958 9.739276 AAAAATAAGGATGTAGTCAGTCAATCA 57.261 29.630 0.00 0.00 0.00 2.57
1838 2002 7.868922 GCATGCATTAATCATGTTTATCCAGAA 59.131 33.333 14.21 0.00 42.34 3.02
1853 2017 0.956633 CGCTCCCTGCATGCATTAAT 59.043 50.000 22.97 0.00 43.06 1.40
1854 2018 0.107263 TCGCTCCCTGCATGCATTAA 60.107 50.000 22.97 8.32 43.06 1.40
1889 2059 1.518774 GATGTTGGGCATTGGGCTG 59.481 57.895 0.00 0.00 44.01 4.85
2103 2273 1.353694 AGCTTGATCCAGAGGCTTGTT 59.646 47.619 0.00 0.00 0.00 2.83
2224 2394 5.105837 GGTTGACTAGTAGGAGTAACAGTGG 60.106 48.000 0.00 0.00 0.00 4.00
2227 2397 5.711036 ACAGGTTGACTAGTAGGAGTAACAG 59.289 44.000 0.00 1.73 0.00 3.16
2228 2398 5.475909 CACAGGTTGACTAGTAGGAGTAACA 59.524 44.000 0.00 0.00 0.00 2.41
2300 2489 0.031178 GTCCCAGTGAACACGTACGT 59.969 55.000 16.72 16.72 36.20 3.57
2301 2490 0.313043 AGTCCCAGTGAACACGTACG 59.687 55.000 15.01 15.01 36.20 3.67
2302 2491 1.612463 AGAGTCCCAGTGAACACGTAC 59.388 52.381 0.00 0.00 36.20 3.67
2303 2492 1.611977 CAGAGTCCCAGTGAACACGTA 59.388 52.381 0.00 0.00 36.20 3.57
2343 2536 0.452452 GACACGTCGACGGTCTTCTC 60.452 60.000 37.89 19.47 44.95 2.87
2403 2598 1.458486 CAGGTAGGTGGGCCACAAA 59.542 57.895 35.69 21.26 35.86 2.83
2404 2599 3.166434 CAGGTAGGTGGGCCACAA 58.834 61.111 35.69 21.63 35.86 3.33
2468 2663 6.258068 CAGGAATGAAAATAGTACGAGGTTCC 59.742 42.308 0.00 0.00 33.38 3.62
2553 2748 5.868454 TCAGACAATCAAGATCAACCAAGA 58.132 37.500 0.00 0.00 0.00 3.02
2582 2781 9.550406 GCAAGATCTAGTATCTATATACTCCGT 57.450 37.037 4.17 0.00 44.05 4.69
2583 2782 8.995220 GGCAAGATCTAGTATCTATATACTCCG 58.005 40.741 4.17 0.00 44.05 4.63
2584 2783 8.995220 CGGCAAGATCTAGTATCTATATACTCC 58.005 40.741 4.17 0.00 44.05 3.85
2696 2895 3.683365 CCAAAATGGTGGGAAAAGGAG 57.317 47.619 0.00 0.00 34.77 3.69
2778 2977 3.950794 TTTCCTGCCGCCGCTACTG 62.951 63.158 0.00 0.00 35.36 2.74
2779 2978 2.741486 TTTTTCCTGCCGCCGCTACT 62.741 55.000 0.00 0.00 35.36 2.57
2780 2979 2.253414 CTTTTTCCTGCCGCCGCTAC 62.253 60.000 0.00 0.00 35.36 3.58
2781 2980 2.032834 TTTTTCCTGCCGCCGCTA 59.967 55.556 0.00 0.00 35.36 4.26
2782 2981 3.365265 CTTTTTCCTGCCGCCGCT 61.365 61.111 0.00 0.00 35.36 5.52
2783 2982 4.419939 CCTTTTTCCTGCCGCCGC 62.420 66.667 0.00 0.00 0.00 6.53
2784 2983 2.265182 TTCCTTTTTCCTGCCGCCG 61.265 57.895 0.00 0.00 0.00 6.46
2785 2984 1.289066 GTTCCTTTTTCCTGCCGCC 59.711 57.895 0.00 0.00 0.00 6.13
2786 2985 1.081442 CGTTCCTTTTTCCTGCCGC 60.081 57.895 0.00 0.00 0.00 6.53
2787 2986 1.081442 GCGTTCCTTTTTCCTGCCG 60.081 57.895 0.00 0.00 0.00 5.69
2788 2987 1.289066 GGCGTTCCTTTTTCCTGCC 59.711 57.895 0.00 0.00 0.00 4.85
2789 2988 1.289066 GGGCGTTCCTTTTTCCTGC 59.711 57.895 0.00 0.00 0.00 4.85
2790 2989 0.825840 TGGGGCGTTCCTTTTTCCTG 60.826 55.000 0.00 0.00 35.33 3.86
2791 2990 0.539669 CTGGGGCGTTCCTTTTTCCT 60.540 55.000 0.00 0.00 35.33 3.36
2792 2991 1.532604 CCTGGGGCGTTCCTTTTTCC 61.533 60.000 0.00 0.00 35.33 3.13
2793 2992 1.964448 CCTGGGGCGTTCCTTTTTC 59.036 57.895 0.00 0.00 35.33 2.29
2794 2993 2.207229 GCCTGGGGCGTTCCTTTTT 61.207 57.895 0.00 0.00 39.62 1.94
2795 2994 2.600470 GCCTGGGGCGTTCCTTTT 60.600 61.111 0.00 0.00 39.62 2.27
2808 3007 3.333219 TTCCCTGGAGGCTGCCTG 61.333 66.667 28.82 12.02 31.76 4.85
2809 3008 3.334054 GTTCCCTGGAGGCTGCCT 61.334 66.667 23.64 23.64 36.03 4.75
2810 3009 3.334054 AGTTCCCTGGAGGCTGCC 61.334 66.667 11.65 11.65 34.51 4.85
2811 3010 1.553690 TACAGTTCCCTGGAGGCTGC 61.554 60.000 15.35 0.00 43.36 5.25
2812 3011 0.539051 CTACAGTTCCCTGGAGGCTG 59.461 60.000 14.39 14.39 44.74 4.85
2813 3012 2.998493 CTACAGTTCCCTGGAGGCT 58.002 57.895 0.00 0.00 44.74 4.58
2817 3016 0.976641 CAGTGCTACAGTTCCCTGGA 59.023 55.000 0.00 0.00 43.36 3.86
2818 3017 0.687354 ACAGTGCTACAGTTCCCTGG 59.313 55.000 0.00 0.00 43.36 4.45
2819 3018 2.675317 GCTACAGTGCTACAGTTCCCTG 60.675 54.545 0.00 0.00 44.68 4.45
2820 3019 1.550976 GCTACAGTGCTACAGTTCCCT 59.449 52.381 0.00 0.00 0.00 4.20
2821 3020 1.550976 AGCTACAGTGCTACAGTTCCC 59.449 52.381 0.00 0.00 42.10 3.97
2837 3036 4.202121 GGCATTGTAGCAGTACTGTAGCTA 60.202 45.833 23.44 15.74 39.68 3.32
2838 3037 3.430929 GGCATTGTAGCAGTACTGTAGCT 60.431 47.826 23.44 16.74 42.14 3.32
2839 3038 2.866762 GGCATTGTAGCAGTACTGTAGC 59.133 50.000 23.44 15.43 35.83 3.58
2840 3039 3.118775 TGGGCATTGTAGCAGTACTGTAG 60.119 47.826 23.44 7.61 35.83 2.74
2841 3040 2.835156 TGGGCATTGTAGCAGTACTGTA 59.165 45.455 23.44 11.96 35.83 2.74
2842 3041 1.628340 TGGGCATTGTAGCAGTACTGT 59.372 47.619 23.44 12.90 35.83 3.55
2843 3042 2.401583 TGGGCATTGTAGCAGTACTG 57.598 50.000 18.93 18.93 35.83 2.74
2844 3043 3.009033 TCTTTGGGCATTGTAGCAGTACT 59.991 43.478 0.00 0.00 35.83 2.73
2845 3044 3.343617 TCTTTGGGCATTGTAGCAGTAC 58.656 45.455 0.00 0.00 35.83 2.73
2846 3045 3.712016 TCTTTGGGCATTGTAGCAGTA 57.288 42.857 0.00 0.00 35.83 2.74
2847 3046 2.584835 TCTTTGGGCATTGTAGCAGT 57.415 45.000 0.00 0.00 35.83 4.40
2848 3047 3.940209 TTTCTTTGGGCATTGTAGCAG 57.060 42.857 0.00 0.00 35.83 4.24
2849 3048 4.567971 CATTTTCTTTGGGCATTGTAGCA 58.432 39.130 0.00 0.00 35.83 3.49
2850 3049 3.371898 GCATTTTCTTTGGGCATTGTAGC 59.628 43.478 0.00 0.00 0.00 3.58
2851 3050 4.567971 TGCATTTTCTTTGGGCATTGTAG 58.432 39.130 0.00 0.00 0.00 2.74
2852 3051 4.613925 TGCATTTTCTTTGGGCATTGTA 57.386 36.364 0.00 0.00 0.00 2.41
2853 3052 3.488778 TGCATTTTCTTTGGGCATTGT 57.511 38.095 0.00 0.00 0.00 2.71
2854 3053 4.258543 AGATGCATTTTCTTTGGGCATTG 58.741 39.130 0.00 0.00 44.52 2.82
2855 3054 4.020039 TGAGATGCATTTTCTTTGGGCATT 60.020 37.500 0.00 0.00 44.52 3.56
2856 3055 3.516300 TGAGATGCATTTTCTTTGGGCAT 59.484 39.130 0.00 0.00 46.91 4.40
2857 3056 2.898612 TGAGATGCATTTTCTTTGGGCA 59.101 40.909 0.00 0.00 39.03 5.36
2858 3057 3.256558 GTGAGATGCATTTTCTTTGGGC 58.743 45.455 0.00 0.00 0.00 5.36
2859 3058 3.504863 CGTGAGATGCATTTTCTTTGGG 58.495 45.455 0.00 0.00 0.00 4.12
2860 3059 2.919229 GCGTGAGATGCATTTTCTTTGG 59.081 45.455 0.00 0.00 0.00 3.28
2861 3060 2.919229 GGCGTGAGATGCATTTTCTTTG 59.081 45.455 0.00 0.00 0.00 2.77
2862 3061 2.094545 GGGCGTGAGATGCATTTTCTTT 60.095 45.455 0.00 0.00 0.00 2.52
2863 3062 1.474077 GGGCGTGAGATGCATTTTCTT 59.526 47.619 0.00 0.00 0.00 2.52
2864 3063 1.098050 GGGCGTGAGATGCATTTTCT 58.902 50.000 0.00 0.00 0.00 2.52
2865 3064 0.101219 GGGGCGTGAGATGCATTTTC 59.899 55.000 0.00 2.76 0.00 2.29
2866 3065 0.611618 TGGGGCGTGAGATGCATTTT 60.612 50.000 0.00 0.00 0.00 1.82
2867 3066 1.001020 TGGGGCGTGAGATGCATTT 60.001 52.632 0.00 0.00 0.00 2.32
2868 3067 1.452651 CTGGGGCGTGAGATGCATT 60.453 57.895 0.00 0.00 0.00 3.56
2869 3068 2.191375 CTGGGGCGTGAGATGCAT 59.809 61.111 0.00 0.00 0.00 3.96
2870 3069 4.100084 CCTGGGGCGTGAGATGCA 62.100 66.667 0.00 0.00 0.00 3.96
2919 3118 2.106332 ATACGTAGGCGCAGTGGC 59.894 61.111 10.83 0.00 42.83 5.01
2920 3119 2.237751 GCATACGTAGGCGCAGTGG 61.238 63.158 17.16 0.00 42.83 4.00
2921 3120 2.237751 GGCATACGTAGGCGCAGTG 61.238 63.158 24.13 5.96 42.83 3.66
2922 3121 1.956629 AAGGCATACGTAGGCGCAGT 61.957 55.000 24.13 7.55 42.83 4.40
2923 3122 1.215655 GAAGGCATACGTAGGCGCAG 61.216 60.000 24.13 0.00 42.83 5.18
2924 3123 1.227147 GAAGGCATACGTAGGCGCA 60.227 57.895 24.13 0.00 42.83 6.09
2925 3124 1.954651 GGAAGGCATACGTAGGCGC 60.955 63.158 24.13 17.16 42.83 6.53
2926 3125 0.104304 AAGGAAGGCATACGTAGGCG 59.896 55.000 24.13 5.66 44.93 5.52
2927 3126 3.464111 TTAAGGAAGGCATACGTAGGC 57.536 47.619 23.23 23.23 0.00 3.93
2928 3127 7.215085 ACTTAATTAAGGAAGGCATACGTAGG 58.785 38.462 25.25 2.16 37.62 3.18
2929 3128 8.658499 AACTTAATTAAGGAAGGCATACGTAG 57.342 34.615 25.25 0.00 37.62 3.51
2930 3129 8.885722 CAAACTTAATTAAGGAAGGCATACGTA 58.114 33.333 25.25 0.00 37.62 3.57
2931 3130 7.392393 ACAAACTTAATTAAGGAAGGCATACGT 59.608 33.333 25.25 0.00 37.62 3.57
2932 3131 7.696453 CACAAACTTAATTAAGGAAGGCATACG 59.304 37.037 25.25 7.45 37.62 3.06
3108 3307 9.218440 CCGTTAAAACTACTTTTACCTTCCATA 57.782 33.333 0.00 0.00 32.59 2.74
3119 3318 6.870971 TGCTTCATCCGTTAAAACTACTTT 57.129 33.333 0.00 0.00 0.00 2.66
3129 3328 3.521560 CTGCTAGTTGCTTCATCCGTTA 58.478 45.455 0.00 0.00 43.37 3.18
3138 3337 1.731720 GCACTAGCTGCTAGTTGCTT 58.268 50.000 33.50 14.18 43.82 3.91
3140 3339 0.458543 TCGCACTAGCTGCTAGTTGC 60.459 55.000 33.50 32.41 43.82 4.17
3144 3343 0.030101 GGAGTCGCACTAGCTGCTAG 59.970 60.000 29.91 29.91 44.64 3.42
3147 3346 1.807573 GTGGAGTCGCACTAGCTGC 60.808 63.158 0.00 7.10 43.21 5.25
3148 3347 1.153745 GGTGGAGTCGCACTAGCTG 60.154 63.158 0.00 0.00 39.10 4.24
3149 3348 0.034380 TAGGTGGAGTCGCACTAGCT 60.034 55.000 10.38 0.00 39.10 3.32
3150 3349 1.033574 ATAGGTGGAGTCGCACTAGC 58.966 55.000 10.38 0.00 37.42 3.42


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

AutoCloner maintained by Alex Coulton.