Multiple sequence alignment - TraesCS3B01G095900

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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 TraesCS3B01G095900 chr3B 100.000 3953 0 0 1 3953 64313648 64317600 0.000000e+00 7300.0
1 TraesCS3B01G095900 chr3B 91.811 403 19 10 1 402 671137108 671136719 2.080000e-152 549.0
2 TraesCS3B01G095900 chr3B 71.875 544 115 31 1648 2175 42125807 42126328 5.360000e-24 122.0
3 TraesCS3B01G095900 chr3B 80.672 119 23 0 1341 1459 41800438 41800556 4.210000e-15 93.5
4 TraesCS3B01G095900 chr3B 80.000 125 25 0 1347 1471 42048068 42047944 4.210000e-15 93.5
5 TraesCS3B01G095900 chr3A 93.569 2628 118 25 981 3570 52457492 52460106 0.000000e+00 3869.0
6 TraesCS3B01G095900 chr3A 92.411 224 9 2 3737 3953 52460792 52461014 2.970000e-81 313.0
7 TraesCS3B01G095900 chr3A 91.429 175 9 4 3566 3737 52460585 52460756 6.600000e-58 235.0
8 TraesCS3B01G095900 chr3A 90.000 90 4 4 873 958 52457303 52457391 1.160000e-20 111.0
9 TraesCS3B01G095900 chr3A 79.259 135 28 0 1348 1482 32876385 32876251 1.170000e-15 95.3
10 TraesCS3B01G095900 chr3A 73.026 304 64 15 1648 1942 32876109 32875815 1.510000e-14 91.6
11 TraesCS3B01G095900 chr3D 92.755 2581 128 30 964 3511 40754824 40752270 0.000000e+00 3675.0
12 TraesCS3B01G095900 chr3D 89.823 226 13 4 3737 3953 40752071 40751847 8.360000e-72 281.0
13 TraesCS3B01G095900 chr3D 92.500 80 4 2 3624 3701 40752212 40752133 3.230000e-21 113.0
14 TraesCS3B01G095900 chr3D 80.153 131 26 0 1353 1483 23730927 23730797 9.040000e-17 99.0
15 TraesCS3B01G095900 chr3D 70.890 584 125 33 1613 2175 23230453 23229894 1.170000e-15 95.3
16 TraesCS3B01G095900 chr3D 93.548 62 4 0 2114 2175 23730193 23730132 4.210000e-15 93.5
17 TraesCS3B01G095900 chr3D 88.158 76 9 0 2113 2188 501162931 501162856 1.510000e-14 91.6
18 TraesCS3B01G095900 chr3D 94.737 57 3 0 1404 1460 23230638 23230582 5.440000e-14 89.8
19 TraesCS3B01G095900 chr3D 79.832 119 24 0 1341 1459 23857931 23858049 1.960000e-13 87.9
20 TraesCS3B01G095900 chr6B 84.403 904 72 33 13 880 6840916 6841786 0.000000e+00 824.0
21 TraesCS3B01G095900 chr6B 83.929 896 80 32 24 877 551981778 551980905 0.000000e+00 798.0
22 TraesCS3B01G095900 chr6B 83.778 900 80 36 1 879 98594354 98593500 0.000000e+00 793.0
23 TraesCS3B01G095900 chr6B 88.519 601 52 10 1745 2336 157534744 157535336 0.000000e+00 712.0
24 TraesCS3B01G095900 chr6B 92.308 403 17 10 1 402 704690703 704691092 9.590000e-156 560.0
25 TraesCS3B01G095900 chr4A 84.056 922 78 38 1 877 690140173 690141070 0.000000e+00 824.0
26 TraesCS3B01G095900 chr5B 94.410 483 22 3 396 877 115375259 115375737 0.000000e+00 737.0
27 TraesCS3B01G095900 chr5B 93.802 484 22 6 396 877 312268598 312269075 0.000000e+00 721.0
28 TraesCS3B01G095900 chr5B 94.420 448 19 3 431 877 711741414 711741856 0.000000e+00 684.0
29 TraesCS3B01G095900 chr5B 92.804 403 15 10 1 402 706379418 706379029 4.430000e-159 571.0
30 TraesCS3B01G095900 chr5B 86.842 76 10 0 2113 2188 426559059 426558984 7.040000e-13 86.1
31 TraesCS3B01G095900 chr5B 81.250 96 12 5 1403 1495 665172893 665172801 5.480000e-09 73.1
32 TraesCS3B01G095900 chr5B 83.133 83 10 4 1403 1483 665540073 665540153 5.480000e-09 73.1
33 TraesCS3B01G095900 chr2B 90.323 496 27 6 396 879 794227149 794227635 7.210000e-177 630.0
34 TraesCS3B01G095900 chr2B 92.556 403 16 10 1 402 752931184 752930795 2.060000e-157 566.0
35 TraesCS3B01G095900 chr2B 92.060 403 18 10 1 402 617149190 617149579 4.460000e-154 555.0
36 TraesCS3B01G095900 chr7B 93.431 411 23 3 469 877 7564781 7564373 1.210000e-169 606.0
37 TraesCS3B01G095900 chr7B 92.308 403 17 10 1 402 564175664 564175275 9.590000e-156 560.0
38 TraesCS3B01G095900 chr7B 92.060 403 18 10 1 402 699154038 699154427 4.460000e-154 555.0
39 TraesCS3B01G095900 chr1B 92.804 403 15 10 1 402 25817871 25818260 4.430000e-159 571.0
40 TraesCS3B01G095900 chr1B 91.811 403 19 10 1 402 672156068 672156457 2.080000e-152 549.0
41 TraesCS3B01G095900 chr1B 89.130 184 17 2 2106 2289 168586363 168586543 3.970000e-55 226.0
42 TraesCS3B01G095900 chr4B 71.757 609 140 23 1602 2188 672129512 672128914 4.120000e-30 143.0
43 TraesCS3B01G095900 chr4B 90.741 54 5 0 1401 1454 631574982 631574929 5.480000e-09 73.1
44 TraesCS3B01G095900 chrUn 71.644 596 142 19 1602 2179 100089955 100090541 5.330000e-29 139.0
45 TraesCS3B01G095900 chrUn 80.000 125 25 0 1347 1471 373565392 373565268 4.210000e-15 93.5
46 TraesCS3B01G095900 chr5A 90.667 75 7 0 2105 2179 658990149 658990223 2.510000e-17 100.0
47 TraesCS3B01G095900 chr5A 82.292 96 11 6 1392 1483 656671407 656671500 1.180000e-10 78.7
48 TraesCS3B01G095900 chr2D 93.443 61 4 0 2115 2175 553252396 553252336 1.510000e-14 91.6
49 TraesCS3B01G095900 chr2D 73.030 330 59 22 1858 2175 528099440 528099129 5.440000e-14 89.8
50 TraesCS3B01G095900 chr2D 94.643 56 3 0 1404 1459 528099870 528099815 1.960000e-13 87.9
51 TraesCS3B01G095900 chr6D 93.333 60 1 2 2230 2289 19349237 19349293 7.040000e-13 86.1
52 TraesCS3B01G095900 chr6D 97.368 38 1 0 1414 1451 22174966 22174929 9.170000e-07 65.8
53 TraesCS3B01G095900 chr7D 92.982 57 1 2 2233 2289 49493304 49493251 3.270000e-11 80.5
54 TraesCS3B01G095900 chr7D 90.909 55 2 2 2235 2289 49427280 49427229 1.970000e-08 71.3
55 TraesCS3B01G095900 chr5D 91.667 60 2 1 2230 2289 561620146 561620090 3.270000e-11 80.5
56 TraesCS3B01G095900 chr5D 82.474 97 9 8 1392 1483 528587519 528587612 1.180000e-10 78.7
57 TraesCS3B01G095900 chr5D 81.443 97 10 8 1392 1483 528415559 528415652 5.480000e-09 73.1
58 TraesCS3B01G095900 chr1A 92.453 53 4 0 1404 1456 257960458 257960510 4.240000e-10 76.8


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 TraesCS3B01G095900 chr3B 64313648 64317600 3952 False 7300.000000 7300 100.000000 1 3953 1 chr3B.!!$F3 3952
1 TraesCS3B01G095900 chr3A 52457303 52461014 3711 False 1132.000000 3869 91.852250 873 3953 4 chr3A.!!$F1 3080
2 TraesCS3B01G095900 chr3D 40751847 40754824 2977 True 1356.333333 3675 91.692667 964 3953 3 chr3D.!!$R4 2989
3 TraesCS3B01G095900 chr6B 6840916 6841786 870 False 824.000000 824 84.403000 13 880 1 chr6B.!!$F1 867
4 TraesCS3B01G095900 chr6B 551980905 551981778 873 True 798.000000 798 83.929000 24 877 1 chr6B.!!$R2 853
5 TraesCS3B01G095900 chr6B 98593500 98594354 854 True 793.000000 793 83.778000 1 879 1 chr6B.!!$R1 878
6 TraesCS3B01G095900 chr6B 157534744 157535336 592 False 712.000000 712 88.519000 1745 2336 1 chr6B.!!$F2 591
7 TraesCS3B01G095900 chr4A 690140173 690141070 897 False 824.000000 824 84.056000 1 877 1 chr4A.!!$F1 876

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
972 1193 0.177604 CATGGCAGAGACCTCTCCAC 59.822 60.0 15.45 3.88 43.88 4.02 F
1057 1359 0.179000 CAAGGAGATCAAGTCCCCGG 59.821 60.0 0.00 0.00 34.21 5.73 F
2581 2925 1.043116 CCAGTACTGCCTCATCGGGA 61.043 60.0 17.86 0.00 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2833 3177 0.319641 AGGAAGACGGCGAAGTTGAC 60.320 55.0 16.62 0.00 0.00 3.18 R
2868 3212 1.421382 GCGGCGTTCTGTACTTGTAA 58.579 50.0 9.37 0.00 0.00 2.41 R
3854 4766 0.102844 TGCAGCAAGGTTGAAGCAAC 59.897 50.0 0.00 1.82 42.89 4.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 102 2.283821 GGCATGGGTGGCTTTGGA 60.284 61.111 0.00 0.00 46.64 3.53
71 103 2.649129 GGCATGGGTGGCTTTGGAC 61.649 63.158 0.00 0.00 46.64 4.02
72 104 2.993471 GCATGGGTGGCTTTGGACG 61.993 63.158 0.00 0.00 0.00 4.79
73 105 2.676471 ATGGGTGGCTTTGGACGC 60.676 61.111 0.00 0.00 0.00 5.19
74 106 3.505790 ATGGGTGGCTTTGGACGCA 62.506 57.895 0.00 0.00 39.11 5.24
75 107 2.676471 GGGTGGCTTTGGACGCAT 60.676 61.111 0.00 0.00 31.42 4.73
76 108 2.568090 GGTGGCTTTGGACGCATG 59.432 61.111 0.00 0.00 31.42 4.06
77 109 2.568090 GTGGCTTTGGACGCATGG 59.432 61.111 0.00 0.00 0.00 3.66
78 110 2.676121 TGGCTTTGGACGCATGGG 60.676 61.111 8.44 8.44 0.00 4.00
79 111 2.361104 GGCTTTGGACGCATGGGA 60.361 61.111 17.76 0.00 0.00 4.37
80 112 2.409870 GGCTTTGGACGCATGGGAG 61.410 63.158 17.76 3.89 0.00 4.30
81 113 2.409870 GCTTTGGACGCATGGGAGG 61.410 63.158 17.76 0.00 0.00 4.30
82 114 2.361104 TTTGGACGCATGGGAGGC 60.361 61.111 17.76 5.23 0.00 4.70
83 115 3.203086 TTTGGACGCATGGGAGGCA 62.203 57.895 17.76 0.00 0.00 4.75
84 116 2.497792 TTTGGACGCATGGGAGGCAT 62.498 55.000 17.76 0.00 0.00 4.40
85 117 2.903855 GGACGCATGGGAGGCATG 60.904 66.667 17.76 0.00 0.00 4.06
86 118 2.903855 GACGCATGGGAGGCATGG 60.904 66.667 17.76 0.00 0.00 3.66
87 119 4.511246 ACGCATGGGAGGCATGGG 62.511 66.667 17.76 0.08 44.99 4.00
88 120 4.511246 CGCATGGGAGGCATGGGT 62.511 66.667 3.11 0.00 37.94 4.51
89 121 2.836360 GCATGGGAGGCATGGGTG 60.836 66.667 0.00 0.00 0.00 4.61
119 175 2.123597 CCATGGGAGGCATGGGTG 60.124 66.667 2.85 0.00 44.32 4.61
120 176 2.123597 CATGGGAGGCATGGGTGG 60.124 66.667 0.00 0.00 0.00 4.61
127 183 2.283821 GGCATGGGTGGCTTTGGA 60.284 61.111 0.00 0.00 46.64 3.53
128 184 2.353610 GGCATGGGTGGCTTTGGAG 61.354 63.158 0.00 0.00 46.64 3.86
129 185 2.353610 GCATGGGTGGCTTTGGAGG 61.354 63.158 0.00 0.00 0.00 4.30
137 193 3.930504 GCTTTGGAGGCATGGGAG 58.069 61.111 0.00 0.00 0.00 4.30
138 194 1.755783 GCTTTGGAGGCATGGGAGG 60.756 63.158 0.00 0.00 0.00 4.30
139 195 1.755783 CTTTGGAGGCATGGGAGGC 60.756 63.158 0.00 0.00 0.00 4.70
140 196 2.503846 CTTTGGAGGCATGGGAGGCA 62.504 60.000 0.00 0.00 36.37 4.75
141 197 1.877672 TTTGGAGGCATGGGAGGCAT 61.878 55.000 0.00 0.00 36.37 4.40
142 198 2.203451 GGAGGCATGGGAGGCATG 60.203 66.667 0.00 0.00 36.37 4.06
143 199 2.203451 GAGGCATGGGAGGCATGG 60.203 66.667 0.00 0.00 36.37 3.66
144 200 3.804638 GAGGCATGGGAGGCATGGG 62.805 68.421 0.00 0.00 36.37 4.00
145 201 4.147587 GGCATGGGAGGCATGGGT 62.148 66.667 0.00 0.00 0.00 4.51
146 202 2.836360 GCATGGGAGGCATGGGTG 60.836 66.667 0.00 0.00 0.00 4.61
281 407 3.672913 CCATGGGAGGCATGGGTA 58.327 61.111 2.85 0.00 44.32 3.69
290 425 2.363975 GGCATGGGTACACCTCCGA 61.364 63.158 0.00 0.00 41.11 4.55
411 619 3.998672 GGCCACCACCGTCGAAGA 61.999 66.667 0.00 0.00 0.00 2.87
425 633 2.860136 GTCGAAGATTCACATGATGCGA 59.140 45.455 0.00 0.00 40.67 5.10
593 802 4.709397 TGAACTTGGTTGGATGAACTTGTT 59.291 37.500 0.00 0.00 34.66 2.83
605 814 6.014755 TGGATGAACTTGTTGGCATGATTTTA 60.015 34.615 0.00 0.00 0.00 1.52
691 900 9.545105 TCATTTTTGTCCAAAATATCCATATGC 57.455 29.630 6.06 0.00 42.28 3.14
692 901 8.776470 CATTTTTGTCCAAAATATCCATATGCC 58.224 33.333 6.06 0.00 42.28 4.40
693 902 6.418057 TTTGTCCAAAATATCCATATGCCC 57.582 37.500 0.00 0.00 0.00 5.36
694 903 5.072129 TGTCCAAAATATCCATATGCCCA 57.928 39.130 0.00 0.00 0.00 5.36
695 904 5.653346 TGTCCAAAATATCCATATGCCCAT 58.347 37.500 0.00 0.00 0.00 4.00
696 905 6.798766 TGTCCAAAATATCCATATGCCCATA 58.201 36.000 0.00 0.00 0.00 2.74
697 906 7.420856 TGTCCAAAATATCCATATGCCCATAT 58.579 34.615 0.00 0.00 34.50 1.78
893 1110 5.034852 TGCTCTAATGCTGCCATTAACTA 57.965 39.130 0.00 0.00 41.88 2.24
894 1111 4.816385 TGCTCTAATGCTGCCATTAACTAC 59.184 41.667 0.00 0.00 41.88 2.73
902 1119 3.118223 GCTGCCATTAACTACCTCCTTCT 60.118 47.826 0.00 0.00 0.00 2.85
910 1127 6.661304 TTAACTACCTCCTTCTTTTCTCGT 57.339 37.500 0.00 0.00 0.00 4.18
916 1133 2.218603 TCCTTCTTTTCTCGTTGCCAC 58.781 47.619 0.00 0.00 0.00 5.01
958 1179 4.899239 CGCTCCCGTCTCCATGGC 62.899 72.222 6.96 0.00 0.00 4.40
959 1180 3.785859 GCTCCCGTCTCCATGGCA 61.786 66.667 6.96 0.00 0.00 4.92
960 1181 2.503061 CTCCCGTCTCCATGGCAG 59.497 66.667 6.96 5.86 0.00 4.85
961 1182 2.038813 TCCCGTCTCCATGGCAGA 59.961 61.111 6.96 8.32 0.00 4.26
962 1183 2.025767 CTCCCGTCTCCATGGCAGAG 62.026 65.000 6.96 0.00 0.00 3.35
963 1184 2.060383 CCCGTCTCCATGGCAGAGA 61.060 63.158 6.96 1.55 38.05 3.10
968 1189 0.337773 TCTCCATGGCAGAGACCTCT 59.662 55.000 6.96 0.00 41.37 3.69
969 1190 0.752054 CTCCATGGCAGAGACCTCTC 59.248 60.000 6.96 0.00 43.17 3.20
971 1192 0.979709 CCATGGCAGAGACCTCTCCA 60.980 60.000 15.46 15.46 43.88 3.86
972 1193 0.177604 CATGGCAGAGACCTCTCCAC 59.822 60.000 15.45 3.88 43.88 4.02
986 1285 2.099921 CTCTCCACCGAATCGACTGAAT 59.900 50.000 3.36 0.00 0.00 2.57
1053 1355 0.915364 AGGCCAAGGAGATCAAGTCC 59.085 55.000 5.01 0.00 0.00 3.85
1057 1359 0.179000 CAAGGAGATCAAGTCCCCGG 59.821 60.000 0.00 0.00 34.21 5.73
1476 1793 1.153745 CACCACGCTCTACCTGCTC 60.154 63.158 0.00 0.00 0.00 4.26
1611 1928 2.103736 GCGTACCTCTACACGGCC 59.896 66.667 0.00 0.00 38.57 6.13
1626 1943 4.509737 GCCCTCTACGTCACGGCC 62.510 72.222 0.35 0.00 33.30 6.13
2094 2417 4.180946 CTCCGGCTCGACGACCTG 62.181 72.222 0.00 3.92 35.47 4.00
2097 2420 4.180946 CGGCTCGACGACCTGGAG 62.181 72.222 0.00 0.00 35.47 3.86
2100 2423 2.045242 CTCGACGACCTGGAGGGA 60.045 66.667 0.00 0.00 40.27 4.20
2581 2925 1.043116 CCAGTACTGCCTCATCGGGA 61.043 60.000 17.86 0.00 0.00 5.14
2787 3131 1.154413 GGCGCAGAACATCAACGTG 60.154 57.895 10.83 0.00 0.00 4.49
2868 3212 1.195115 TCCTCTACTTCGCCAGCATT 58.805 50.000 0.00 0.00 0.00 3.56
2967 3319 8.862325 ACCACAAGTGAATGAATGAAATACTA 57.138 30.769 0.94 0.00 0.00 1.82
2968 3320 8.730680 ACCACAAGTGAATGAATGAAATACTAC 58.269 33.333 0.94 0.00 0.00 2.73
2969 3321 8.950210 CCACAAGTGAATGAATGAAATACTACT 58.050 33.333 0.94 0.00 0.00 2.57
3035 3393 7.861176 TTAAATTGTGGACTAATTTCAACGC 57.139 32.000 0.00 0.00 38.36 4.84
3037 3395 1.801771 TGTGGACTAATTTCAACGCGG 59.198 47.619 12.47 0.00 0.00 6.46
3039 3397 2.481185 GTGGACTAATTTCAACGCGGAA 59.519 45.455 12.47 1.62 0.00 4.30
3040 3398 2.739913 TGGACTAATTTCAACGCGGAAG 59.260 45.455 12.47 0.00 0.00 3.46
3061 3419 7.063662 CGGAAGCAATTTGATCATCATTTTCAA 59.936 33.333 0.00 0.00 0.00 2.69
3120 3478 6.964934 AGTGAAAAATCATTATAACGCCGTTC 59.035 34.615 5.42 0.00 0.00 3.95
3129 3487 1.981254 TAACGCCGTTCGGTTTAGAG 58.019 50.000 5.42 1.44 43.86 2.43
3147 3505 4.899352 AGAGCCAACACAAGTTATCTCT 57.101 40.909 0.00 0.00 39.10 3.10
3208 3569 6.742109 AGATCTCACCAACAACAAAAAGATG 58.258 36.000 0.00 0.00 0.00 2.90
3214 3575 5.459762 CACCAACAACAAAAAGATGCTACAG 59.540 40.000 0.00 0.00 0.00 2.74
3282 3643 5.614324 TCCGATATCACCTCAACTTTGAT 57.386 39.130 3.12 0.00 36.46 2.57
3323 3685 3.665745 ATTCGCAGCCAAAACTGAAAT 57.334 38.095 0.00 0.00 40.25 2.17
3330 3692 4.060205 CAGCCAAAACTGAAATGGAAAGG 58.940 43.478 0.00 0.00 40.25 3.11
3342 3704 8.267183 ACTGAAATGGAAAGGAAAACAAAGATT 58.733 29.630 0.00 0.00 0.00 2.40
3345 3707 9.764363 GAAATGGAAAGGAAAACAAAGATTAGT 57.236 29.630 0.00 0.00 0.00 2.24
3384 3746 3.655276 AGGCAAACAAATTCTGCTCAG 57.345 42.857 0.00 0.00 36.32 3.35
3421 3784 4.543692 CCAAACTAGCATCAATAGCATGC 58.456 43.478 10.51 10.51 46.05 4.06
3511 3892 6.742718 CGATAATTTCAACCAAACAGCACTAG 59.257 38.462 0.00 0.00 0.00 2.57
3512 3893 7.360861 CGATAATTTCAACCAAACAGCACTAGA 60.361 37.037 0.00 0.00 0.00 2.43
3558 3939 3.254166 CACCAGTTTCAATGACCAGGAAG 59.746 47.826 0.00 0.00 0.00 3.46
3578 4442 8.311836 CAGGAAGTACCAATCTAAACTTGACTA 58.688 37.037 0.00 0.00 42.04 2.59
3662 4527 6.620877 AGGTATGTTCAGTCATTCCAGTTA 57.379 37.500 0.00 0.00 37.60 2.24
3663 4528 7.200434 AGGTATGTTCAGTCATTCCAGTTAT 57.800 36.000 0.00 0.00 37.60 1.89
3774 4677 8.477419 AAACAAAGAAGAAAATCCATACCTCA 57.523 30.769 0.00 0.00 0.00 3.86
3854 4766 2.738846 CCGTTCAGTGTTCATTCCTCAG 59.261 50.000 0.00 0.00 0.00 3.35
3888 4800 0.524862 CTGCAACCTGCCTCATTGAC 59.475 55.000 0.00 0.00 44.23 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 97 2.361104 GCCTCCCATGCGTCCAAA 60.361 61.111 0.00 0.00 0.00 3.28
67 99 3.410628 ATGCCTCCCATGCGTCCA 61.411 61.111 0.00 0.00 31.48 4.02
73 105 2.836360 GCACCCATGCCTCCCATG 60.836 66.667 0.00 0.00 46.97 3.66
113 169 2.037847 GCCTCCAAAGCCACCCAT 59.962 61.111 0.00 0.00 0.00 4.00
114 170 2.855770 ATGCCTCCAAAGCCACCCA 61.856 57.895 0.00 0.00 0.00 4.51
115 171 2.037847 ATGCCTCCAAAGCCACCC 59.962 61.111 0.00 0.00 0.00 4.61
118 174 2.037687 CCCATGCCTCCAAAGCCA 59.962 61.111 0.00 0.00 0.00 4.75
119 175 1.755783 CTCCCATGCCTCCAAAGCC 60.756 63.158 0.00 0.00 0.00 4.35
120 176 1.755783 CCTCCCATGCCTCCAAAGC 60.756 63.158 0.00 0.00 0.00 3.51
122 178 1.877672 ATGCCTCCCATGCCTCCAAA 61.878 55.000 0.00 0.00 31.48 3.28
123 179 2.318966 ATGCCTCCCATGCCTCCAA 61.319 57.895 0.00 0.00 31.48 3.53
124 180 2.697263 ATGCCTCCCATGCCTCCA 60.697 61.111 0.00 0.00 31.48 3.86
125 181 2.203451 CATGCCTCCCATGCCTCC 60.203 66.667 0.00 0.00 44.34 4.30
130 186 2.836360 GCACCCATGCCTCCCATG 60.836 66.667 0.00 0.00 46.97 3.66
281 407 4.082523 CATGGCGGTCGGAGGTGT 62.083 66.667 0.00 0.00 0.00 4.16
322 457 4.971125 GCCATAGCGTCGGAGGGC 62.971 72.222 0.00 0.00 0.00 5.19
398 534 0.677288 TGTGAATCTTCGACGGTGGT 59.323 50.000 0.00 0.00 0.00 4.16
408 616 2.032290 CGCATCGCATCATGTGAATCTT 60.032 45.455 4.67 0.00 40.59 2.40
411 619 1.003223 CACGCATCGCATCATGTGAAT 60.003 47.619 4.67 0.00 40.59 2.57
593 802 6.164876 CCACAAGTTCATTAAAATCATGCCA 58.835 36.000 0.00 0.00 0.00 4.92
605 814 3.233507 AGTTCATGCCCACAAGTTCATT 58.766 40.909 0.00 0.00 0.00 2.57
893 1110 2.495084 GCAACGAGAAAAGAAGGAGGT 58.505 47.619 0.00 0.00 0.00 3.85
894 1111 1.807142 GGCAACGAGAAAAGAAGGAGG 59.193 52.381 0.00 0.00 0.00 4.30
902 1119 0.536460 GGAGGGTGGCAACGAGAAAA 60.536 55.000 0.00 0.00 42.51 2.29
910 1127 2.610859 GAGGGAGGAGGGTGGCAA 60.611 66.667 0.00 0.00 0.00 4.52
916 1133 2.965226 TTATGGCGGAGGGAGGAGGG 62.965 65.000 0.00 0.00 0.00 4.30
958 1179 1.407258 GATTCGGTGGAGAGGTCTCTG 59.593 57.143 5.09 0.00 42.48 3.35
959 1180 1.770294 GATTCGGTGGAGAGGTCTCT 58.230 55.000 6.94 0.00 42.48 3.10
960 1181 0.382515 CGATTCGGTGGAGAGGTCTC 59.617 60.000 0.00 0.00 42.14 3.36
961 1182 0.034380 TCGATTCGGTGGAGAGGTCT 60.034 55.000 6.18 0.00 0.00 3.85
962 1183 0.100861 GTCGATTCGGTGGAGAGGTC 59.899 60.000 6.18 0.00 0.00 3.85
963 1184 0.323542 AGTCGATTCGGTGGAGAGGT 60.324 55.000 6.18 0.00 0.00 3.85
964 1185 0.101399 CAGTCGATTCGGTGGAGAGG 59.899 60.000 6.18 0.00 0.00 3.69
965 1186 1.095600 TCAGTCGATTCGGTGGAGAG 58.904 55.000 6.18 0.00 0.00 3.20
966 1187 1.541379 TTCAGTCGATTCGGTGGAGA 58.459 50.000 6.18 0.00 0.00 3.71
968 1189 2.028476 ACAATTCAGTCGATTCGGTGGA 60.028 45.455 6.18 0.00 0.00 4.02
969 1190 2.346803 ACAATTCAGTCGATTCGGTGG 58.653 47.619 6.18 0.00 0.00 4.61
971 1192 3.187700 GCTACAATTCAGTCGATTCGGT 58.812 45.455 6.18 0.00 0.00 4.69
972 1193 2.540101 GGCTACAATTCAGTCGATTCGG 59.460 50.000 6.18 0.00 0.00 4.30
986 1285 2.125310 CCATCACGGCGGCTACAA 60.125 61.111 13.24 0.00 0.00 2.41
1611 1928 1.139095 GAAGGCCGTGACGTAGAGG 59.861 63.158 3.64 0.00 0.00 3.69
1977 2294 3.909662 TCGTAGAGCCCCACGTAC 58.090 61.111 0.00 0.00 39.18 3.67
2092 2415 1.232792 CCTCCTCCTCTCCCTCCAG 59.767 68.421 0.00 0.00 0.00 3.86
2093 2416 1.230650 TCCTCCTCCTCTCCCTCCA 60.231 63.158 0.00 0.00 0.00 3.86
2094 2417 1.231928 GTCCTCCTCCTCTCCCTCC 59.768 68.421 0.00 0.00 0.00 4.30
2095 2418 1.231928 GGTCCTCCTCCTCTCCCTC 59.768 68.421 0.00 0.00 0.00 4.30
2097 2420 2.284151 GGGTCCTCCTCCTCTCCC 59.716 72.222 0.00 0.00 0.00 4.30
2100 2423 2.360980 CACGGGTCCTCCTCCTCT 59.639 66.667 0.00 0.00 0.00 3.69
2581 2925 2.125512 GCAGAACACCTCGGCGAT 60.126 61.111 11.27 0.00 35.47 4.58
2767 3111 1.154413 CGTTGATGTTCTGCGCCAC 60.154 57.895 4.18 0.00 0.00 5.01
2833 3177 0.319641 AGGAAGACGGCGAAGTTGAC 60.320 55.000 16.62 0.00 0.00 3.18
2868 3212 1.421382 GCGGCGTTCTGTACTTGTAA 58.579 50.000 9.37 0.00 0.00 2.41
3035 3393 6.532302 TGAAAATGATGATCAAATTGCTTCCG 59.468 34.615 0.00 0.00 0.00 4.30
3039 3397 9.443323 TCATTTGAAAATGATGATCAAATTGCT 57.557 25.926 13.20 0.00 46.26 3.91
3061 3419 3.121030 GCGCTGTGCTCCGTCATT 61.121 61.111 5.84 0.00 41.73 2.57
3092 3450 6.573725 CGGCGTTATAATGATTTTTCACTAGC 59.426 38.462 8.93 0.00 0.00 3.42
3109 3467 2.533266 CTCTAAACCGAACGGCGTTAT 58.467 47.619 26.87 11.57 39.32 1.89
3113 3471 2.450345 GGCTCTAAACCGAACGGCG 61.450 63.158 13.32 4.80 39.32 6.46
3120 3478 2.218603 ACTTGTGTTGGCTCTAAACCG 58.781 47.619 0.00 0.00 0.00 4.44
3129 3487 3.077359 AGCAGAGATAACTTGTGTTGGC 58.923 45.455 0.00 0.00 37.59 4.52
3147 3505 8.909923 TGTATATAGTTGCAAGTAGTTCTAGCA 58.090 33.333 18.43 8.66 0.00 3.49
3184 3544 6.736794 GCATCTTTTTGTTGTTGGTGAGATCT 60.737 38.462 0.00 0.00 0.00 2.75
3208 3569 8.140628 TCTAGATCAATTGTCAAGATCTGTAGC 58.859 37.037 20.05 0.00 45.79 3.58
3246 3607 6.348050 GGTGATATCGGATTTCAATCAAGAGC 60.348 42.308 11.85 0.00 37.15 4.09
3282 3643 8.177663 GCGAATATTCATCTTTGAGAAGACAAA 58.822 33.333 15.57 0.00 44.27 2.83
3302 3663 4.484236 CATTTCAGTTTTGGCTGCGAATA 58.516 39.130 0.00 0.00 36.49 1.75
3323 3685 7.654022 ACACTAATCTTTGTTTTCCTTTCCA 57.346 32.000 0.00 0.00 0.00 3.53
3330 3692 8.755018 CATCACCAAACACTAATCTTTGTTTTC 58.245 33.333 0.00 0.00 42.04 2.29
3342 3704 3.814625 TGAGTTGCATCACCAAACACTA 58.185 40.909 0.00 0.00 0.00 2.74
3345 3707 2.361757 CCTTGAGTTGCATCACCAAACA 59.638 45.455 0.00 0.00 0.00 2.83
3384 3746 1.024271 TTTGGCCGCAGATATTCAGC 58.976 50.000 0.00 0.00 0.00 4.26
3421 3784 2.959516 TGACTCCTTGCTTGTATCGTG 58.040 47.619 0.00 0.00 0.00 4.35
3511 3892 1.674962 GCCTGCTGGAATCAGAACATC 59.325 52.381 14.77 0.00 43.49 3.06
3512 3893 1.005097 TGCCTGCTGGAATCAGAACAT 59.995 47.619 14.77 0.00 43.49 2.71
3558 3939 9.614792 ATCCAATAGTCAAGTTTAGATTGGTAC 57.385 33.333 10.39 0.00 42.52 3.34
3617 4482 6.166279 CCTTCTTCATACTGAACAGCTGTTA 58.834 40.000 31.20 16.80 38.56 2.41
3618 4483 4.999950 CCTTCTTCATACTGAACAGCTGTT 59.000 41.667 31.57 31.57 41.64 3.16
3619 4484 4.040952 ACCTTCTTCATACTGAACAGCTGT 59.959 41.667 15.25 15.25 32.21 4.40
3686 4553 6.355747 CCCCATGTGCATATTTTTACCAAAT 58.644 36.000 0.00 0.00 0.00 2.32
3717 4584 8.097662 CCTTTTTAGTGTTCCTTCTAGTCATCT 58.902 37.037 0.00 0.00 0.00 2.90
3774 4677 1.476291 GGTCTCTTTGGGTTCACCGTT 60.476 52.381 0.00 0.00 44.64 4.44
3854 4766 0.102844 TGCAGCAAGGTTGAAGCAAC 59.897 50.000 0.00 1.82 42.89 4.17


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

AutoCloner maintained by Alex Coulton.