Multiple sequence alignment - TraesCS7A01G087900

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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 TraesCS7A01G087900 chr7A 100.000 4659 0 0 1 4659 52953997 52949339 0.000000e+00 8604.0
1 TraesCS7A01G087900 chr7A 80.000 115 19 4 3196 3308 622067111 622067223 1.070000e-11 82.4
2 TraesCS7A01G087900 chr4A 94.823 3786 151 17 900 4659 664446196 664442430 0.000000e+00 5864.0
3 TraesCS7A01G087900 chr4A 83.249 591 43 16 156 736 664446904 664446360 4.190000e-135 492.0
4 TraesCS7A01G087900 chr4A 94.286 70 4 0 837 906 664446345 664446276 1.770000e-19 108.0
5 TraesCS7A01G087900 chr4A 100.000 29 0 0 2836 2864 126584525 126584553 2.000000e-03 54.7
6 TraesCS7A01G087900 chr7D 95.321 3227 121 13 900 4111 49828779 49825568 0.000000e+00 5096.0
7 TraesCS7A01G087900 chr7D 92.921 777 30 8 138 905 49829617 49828857 0.000000e+00 1107.0
8 TraesCS7A01G087900 chr5D 77.675 1626 256 59 1408 3021 496134340 496135870 0.000000e+00 893.0
9 TraesCS7A01G087900 chr5D 78.832 411 57 13 2304 2712 496153286 496153668 2.780000e-62 250.0
10 TraesCS7A01G087900 chr5D 78.193 321 63 5 3330 3644 496155471 496155790 1.020000e-46 198.0
11 TraesCS7A01G087900 chr5D 75.806 186 35 7 936 1118 496072961 496073139 8.310000e-13 86.1
12 TraesCS7A01G087900 chr5D 83.158 95 14 2 1025 1118 496280744 496280837 8.310000e-13 86.1
13 TraesCS7A01G087900 chr5D 75.000 184 40 4 936 1118 495906131 495906309 3.860000e-11 80.5
14 TraesCS7A01G087900 chr5A 77.476 1656 258 63 1408 3041 619957173 619958735 0.000000e+00 885.0
15 TraesCS7A01G087900 chr5A 85.057 87 12 1 1033 1118 620166563 620166649 2.310000e-13 87.9
16 TraesCS7A01G087900 chr5A 75.269 186 36 9 936 1118 619957530 619957708 3.860000e-11 80.5
17 TraesCS7A01G087900 chr5B 77.530 1166 188 47 1525 2679 613280671 613281773 6.580000e-178 634.0
18 TraesCS7A01G087900 chr5B 82.353 663 105 8 1403 2060 614051145 614051800 2.430000e-157 566.0
19 TraesCS7A01G087900 chr5B 78.908 403 58 10 2311 2712 613653712 613654088 1.000000e-61 248.0
20 TraesCS7A01G087900 chr5B 93.701 127 6 2 1 126 29926855 29926730 6.150000e-44 189.0
21 TraesCS7A01G087900 chr5B 76.216 185 35 6 936 1118 613280911 613281088 6.420000e-14 89.8
22 TraesCS7A01G087900 chr5B 80.734 109 19 2 1011 1118 613631110 613631217 2.990000e-12 84.2
23 TraesCS7A01G087900 chr4D 77.710 489 96 10 2836 3319 340990103 340989623 2.120000e-73 287.0
24 TraesCS7A01G087900 chr4B 92.800 125 4 3 1 124 517453408 517453288 4.790000e-40 176.0
25 TraesCS7A01G087900 chr4B 76.897 290 55 11 2836 3120 422374955 422374673 2.240000e-33 154.0
26 TraesCS7A01G087900 chr4B 90.244 82 6 2 3082 3162 568489018 568488938 6.380000e-19 106.0
27 TraesCS7A01G087900 chr4B 74.340 265 55 13 1407 1664 68402671 68402929 2.970000e-17 100.0
28 TraesCS7A01G087900 chr3D 92.000 125 8 2 1 124 38430264 38430387 1.720000e-39 174.0
29 TraesCS7A01G087900 chr3B 88.000 100 8 3 25 123 183473790 183473886 1.060000e-21 115.0
30 TraesCS7A01G087900 chr6B 80.172 116 19 4 3199 3312 313220931 313220818 2.990000e-12 84.2
31 TraesCS7A01G087900 chr6B 80.952 105 19 1 3199 3302 62849484 62849380 1.070000e-11 82.4
32 TraesCS7A01G087900 chr6B 79.310 116 19 5 3199 3312 45324422 45324310 5.000000e-10 76.8
33 TraesCS7A01G087900 chr7B 81.132 106 16 4 3199 3302 5827996 5828099 1.070000e-11 82.4
34 TraesCS7A01G087900 chr2A 81.132 106 16 4 3199 3302 358823845 358823742 1.070000e-11 82.4
35 TraesCS7A01G087900 chr2A 79.310 116 19 5 3199 3312 122692436 122692548 5.000000e-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 TraesCS7A01G087900 chr7A 52949339 52953997 4658 True 8604.000000 8604 100.0000 1 4659 1 chr7A.!!$R1 4658
1 TraesCS7A01G087900 chr4A 664442430 664446904 4474 True 2154.666667 5864 90.7860 156 4659 3 chr4A.!!$R1 4503
2 TraesCS7A01G087900 chr7D 49825568 49829617 4049 True 3101.500000 5096 94.1210 138 4111 2 chr7D.!!$R1 3973
3 TraesCS7A01G087900 chr5D 496134340 496135870 1530 False 893.000000 893 77.6750 1408 3021 1 chr5D.!!$F3 1613
4 TraesCS7A01G087900 chr5D 496153286 496155790 2504 False 224.000000 250 78.5125 2304 3644 2 chr5D.!!$F5 1340
5 TraesCS7A01G087900 chr5A 619957173 619958735 1562 False 482.750000 885 76.3725 936 3041 2 chr5A.!!$F2 2105
6 TraesCS7A01G087900 chr5B 614051145 614051800 655 False 566.000000 566 82.3530 1403 2060 1 chr5B.!!$F3 657
7 TraesCS7A01G087900 chr5B 613280671 613281773 1102 False 361.900000 634 76.8730 936 2679 2 chr5B.!!$F4 1743

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
126 127 0.112412 ACAGGGCCCGAATTTTGTCT 59.888 50.0 18.44 0.0 0.00 3.41 F
1456 1667 0.383949 TGCAGCGTTTCAAAAGGGAC 59.616 50.0 0.00 0.0 0.00 4.46 F
3053 4513 0.319083 TACGTGATGTGCCCGTTTCT 59.681 50.0 0.00 0.0 36.12 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 1712 0.323302 TCTTGGCGACCACAATAGCA 59.677 50.0 0.00 0.0 30.78 3.49 R
3148 4608 0.888619 CACCACGTCCTTCTGAGCTA 59.111 55.0 0.00 0.0 0.00 3.32 R
4562 6128 0.804989 AAGCAAAGTACATGGCGCTC 59.195 50.0 7.64 0.0 0.00 5.03 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
37 38 8.475331 GACGGTTTGTCTAATTTTCTATGAGA 57.525 34.615 0.00 0.00 44.58 3.27
38 39 9.099454 GACGGTTTGTCTAATTTTCTATGAGAT 57.901 33.333 0.00 0.00 44.58 2.75
91 92 3.945640 TTTTTAGTGAGATAGGGCCCC 57.054 47.619 21.43 2.42 0.00 5.80
92 93 2.579624 TTTAGTGAGATAGGGCCCCA 57.420 50.000 21.43 4.63 0.00 4.96
93 94 2.815357 TTAGTGAGATAGGGCCCCAT 57.185 50.000 21.43 11.55 0.00 4.00
94 95 2.815357 TAGTGAGATAGGGCCCCATT 57.185 50.000 21.43 8.29 0.00 3.16
95 96 1.912862 AGTGAGATAGGGCCCCATTT 58.087 50.000 21.43 5.23 0.00 2.32
96 97 2.217776 AGTGAGATAGGGCCCCATTTT 58.782 47.619 21.43 0.62 0.00 1.82
97 98 3.403322 AGTGAGATAGGGCCCCATTTTA 58.597 45.455 21.43 3.62 0.00 1.52
98 99 3.990245 AGTGAGATAGGGCCCCATTTTAT 59.010 43.478 21.43 9.52 0.00 1.40
99 100 5.170198 AGTGAGATAGGGCCCCATTTTATA 58.830 41.667 21.43 1.80 0.00 0.98
100 101 5.251700 AGTGAGATAGGGCCCCATTTTATAG 59.748 44.000 21.43 0.00 0.00 1.31
101 102 5.014228 GTGAGATAGGGCCCCATTTTATAGT 59.986 44.000 21.43 0.00 0.00 2.12
102 103 5.615261 TGAGATAGGGCCCCATTTTATAGTT 59.385 40.000 21.43 0.00 0.00 2.24
103 104 6.104094 TGAGATAGGGCCCCATTTTATAGTTT 59.896 38.462 21.43 0.00 0.00 2.66
104 105 6.552932 AGATAGGGCCCCATTTTATAGTTTC 58.447 40.000 21.43 0.00 0.00 2.78
105 106 3.562182 AGGGCCCCATTTTATAGTTTCG 58.438 45.455 21.43 0.00 0.00 3.46
106 107 2.035449 GGGCCCCATTTTATAGTTTCGC 59.965 50.000 12.23 0.00 0.00 4.70
107 108 2.691011 GGCCCCATTTTATAGTTTCGCA 59.309 45.455 0.00 0.00 0.00 5.10
108 109 3.490249 GGCCCCATTTTATAGTTTCGCAC 60.490 47.826 0.00 0.00 0.00 5.34
109 110 3.129638 GCCCCATTTTATAGTTTCGCACA 59.870 43.478 0.00 0.00 0.00 4.57
110 111 4.733523 GCCCCATTTTATAGTTTCGCACAG 60.734 45.833 0.00 0.00 0.00 3.66
111 112 4.202010 CCCCATTTTATAGTTTCGCACAGG 60.202 45.833 0.00 0.00 0.00 4.00
112 113 4.202010 CCCATTTTATAGTTTCGCACAGGG 60.202 45.833 0.00 0.00 0.00 4.45
113 114 4.351192 CATTTTATAGTTTCGCACAGGGC 58.649 43.478 0.00 0.00 39.90 5.19
114 115 2.032680 TTATAGTTTCGCACAGGGCC 57.967 50.000 0.00 0.00 40.31 5.80
115 116 0.179468 TATAGTTTCGCACAGGGCCC 59.821 55.000 16.46 16.46 40.31 5.80
116 117 2.869503 ATAGTTTCGCACAGGGCCCG 62.870 60.000 18.44 14.39 40.31 6.13
118 119 4.257654 TTTCGCACAGGGCCCGAA 62.258 61.111 18.44 13.16 40.31 4.30
119 120 3.561120 TTTCGCACAGGGCCCGAAT 62.561 57.895 18.44 2.15 40.19 3.34
120 121 3.561120 TTCGCACAGGGCCCGAATT 62.561 57.895 18.44 0.00 40.31 2.17
121 122 3.061848 CGCACAGGGCCCGAATTT 61.062 61.111 18.44 0.00 40.31 1.82
122 123 2.635443 CGCACAGGGCCCGAATTTT 61.635 57.895 18.44 0.00 40.31 1.82
123 124 1.079888 GCACAGGGCCCGAATTTTG 60.080 57.895 18.44 10.90 36.11 2.44
124 125 1.815817 GCACAGGGCCCGAATTTTGT 61.816 55.000 18.44 11.67 36.11 2.83
125 126 0.243636 CACAGGGCCCGAATTTTGTC 59.756 55.000 18.44 0.00 0.00 3.18
126 127 0.112412 ACAGGGCCCGAATTTTGTCT 59.888 50.000 18.44 0.00 0.00 3.41
127 128 0.811281 CAGGGCCCGAATTTTGTCTC 59.189 55.000 18.44 0.00 0.00 3.36
128 129 0.404040 AGGGCCCGAATTTTGTCTCA 59.596 50.000 18.44 0.00 0.00 3.27
129 130 1.203001 AGGGCCCGAATTTTGTCTCAA 60.203 47.619 18.44 0.00 0.00 3.02
130 131 1.202348 GGGCCCGAATTTTGTCTCAAG 59.798 52.381 5.69 0.00 0.00 3.02
131 132 2.159382 GGCCCGAATTTTGTCTCAAGA 58.841 47.619 0.00 0.00 0.00 3.02
132 133 2.162408 GGCCCGAATTTTGTCTCAAGAG 59.838 50.000 0.00 0.00 0.00 2.85
133 134 3.074412 GCCCGAATTTTGTCTCAAGAGA 58.926 45.455 0.00 0.00 34.56 3.10
153 154 0.672401 CGTACGTGGATGCAAAGGGT 60.672 55.000 7.22 0.00 0.00 4.34
226 227 4.876679 GGCAACTACTGAAAGGGATCTAAC 59.123 45.833 0.00 0.00 39.30 2.34
267 268 3.076621 ACCCGGTCGTTTAGGAATTTTC 58.923 45.455 0.00 0.00 0.00 2.29
366 371 5.187967 GGAAGGAGAACAGAGGTAAGAATCA 59.812 44.000 0.00 0.00 0.00 2.57
382 387 1.527034 ATCAAATCGCAGCACACACT 58.473 45.000 0.00 0.00 0.00 3.55
643 650 1.681486 TTCTGCTGGTCACCACGTCA 61.681 55.000 0.00 0.00 0.00 4.35
647 654 1.006102 CTGGTCACCACGTCAGGAC 60.006 63.158 0.00 0.38 0.00 3.85
661 672 0.946221 CAGGACGTCAGTTGGCAGAC 60.946 60.000 18.91 0.00 0.00 3.51
742 753 5.122239 TCTCGTGAATTTCCTTGCTACAATG 59.878 40.000 0.00 0.00 0.00 2.82
745 756 5.569059 CGTGAATTTCCTTGCTACAATGTTC 59.431 40.000 0.00 0.00 0.00 3.18
766 777 2.549992 CCGGCCGATTCATGGAGAAATA 60.550 50.000 30.73 0.00 40.22 1.40
798 809 5.392995 TCTCAATCTTTTTCCCATTGTCCA 58.607 37.500 0.00 0.00 0.00 4.02
799 810 5.837979 TCTCAATCTTTTTCCCATTGTCCAA 59.162 36.000 0.00 0.00 0.00 3.53
800 811 6.497954 TCTCAATCTTTTTCCCATTGTCCAAT 59.502 34.615 0.00 0.00 0.00 3.16
801 812 7.016465 TCTCAATCTTTTTCCCATTGTCCAATT 59.984 33.333 0.00 0.00 0.00 2.32
818 829 7.282585 TGTCCAATTAATTCATCTCGAATCCT 58.717 34.615 0.00 0.00 43.83 3.24
865 884 0.393267 AAAATTCCGGCCGGATTCGA 60.393 50.000 45.44 31.93 44.74 3.71
925 1114 8.838365 AGTACTATACAAGTCTTCTTATCGTGG 58.162 37.037 0.00 0.00 39.80 4.94
969 1161 6.019075 TCGCTACAATATATCACTGCAAACAC 60.019 38.462 0.00 0.00 0.00 3.32
990 1186 3.736996 TTTGCACTGCAGGGCCTGT 62.737 57.895 36.82 12.53 40.61 4.00
1104 1300 2.749621 GCTTCTGATTGGTGATTTCCGT 59.250 45.455 0.00 0.00 0.00 4.69
1112 1308 3.912496 TGGTGATTTCCGTGATGAGAT 57.088 42.857 0.00 0.00 0.00 2.75
1113 1309 3.534554 TGGTGATTTCCGTGATGAGATG 58.465 45.455 0.00 0.00 0.00 2.90
1114 1310 2.874701 GGTGATTTCCGTGATGAGATGG 59.125 50.000 0.00 0.00 0.00 3.51
1115 1311 3.535561 GTGATTTCCGTGATGAGATGGT 58.464 45.455 0.00 0.00 0.00 3.55
1116 1312 4.442893 GGTGATTTCCGTGATGAGATGGTA 60.443 45.833 0.00 0.00 0.00 3.25
1117 1313 5.116180 GTGATTTCCGTGATGAGATGGTAA 58.884 41.667 0.00 0.00 0.00 2.85
1118 1314 5.235186 GTGATTTCCGTGATGAGATGGTAAG 59.765 44.000 0.00 0.00 0.00 2.34
1160 1356 2.752354 TCCATTCTTACCGTGCCATTTG 59.248 45.455 0.00 0.00 0.00 2.32
1177 1373 5.815222 GCCATTTGTTTTTGTAAGACCACTT 59.185 36.000 0.00 0.00 39.81 3.16
1200 1398 6.850752 TGACCAGTGATGTTTCTACTATCA 57.149 37.500 0.00 0.00 0.00 2.15
1240 1438 2.489938 TGGTAAGACCAGTGCCATTC 57.510 50.000 0.00 0.00 44.79 2.67
1245 1443 5.007682 GGTAAGACCAGTGCCATTCTTTTA 58.992 41.667 0.00 0.00 38.42 1.52
1305 1505 7.930217 AGTACCAAAATGATATCGGAACATTG 58.070 34.615 0.00 0.00 35.00 2.82
1399 1610 4.327087 CAGTCTGACCAAACTTTTTGTTGC 59.673 41.667 3.76 0.00 39.13 4.17
1433 1644 7.623677 TCTTCCTGTAGATAATCCCAGAAGAAA 59.376 37.037 0.00 0.00 0.00 2.52
1456 1667 0.383949 TGCAGCGTTTCAAAAGGGAC 59.616 50.000 0.00 0.00 0.00 4.46
1523 1734 1.860950 CTATTGTGGTCGCCAAGATCG 59.139 52.381 0.00 0.00 34.18 3.69
2083 2311 5.048504 ACTTTGGAGACATGCACAAACTATG 60.049 40.000 0.00 0.00 42.32 2.23
2189 2418 4.824537 TCAGGTATGCTAGTTTGCACAAAA 59.175 37.500 0.00 0.00 46.33 2.44
2246 2477 7.713073 TGGTTTTCACATTTTTCCTTTGATACC 59.287 33.333 0.00 0.00 0.00 2.73
2399 2637 8.491045 AAAATATTGGTTCTTTTTCTCCAGGA 57.509 30.769 0.00 0.00 0.00 3.86
2494 2732 2.483877 CGCAGCTACAAAATTGGAGTCA 59.516 45.455 7.20 0.00 41.33 3.41
2513 2751 6.183360 GGAGTCACCGAGAACAAACTAGATAT 60.183 42.308 0.00 0.00 0.00 1.63
2653 2891 6.204688 TGTCATAATCTTCGATAAACATGGCC 59.795 38.462 0.00 0.00 0.00 5.36
2685 2923 5.705905 GGCATTATCAGTTATTGTAGACCCC 59.294 44.000 0.00 0.00 0.00 4.95
3016 4476 3.330701 TGCACAGGAGGTTCTTTATCCTT 59.669 43.478 0.00 0.00 41.60 3.36
3029 4489 4.706476 TCTTTATCCTTTGAACATGGCCAG 59.294 41.667 13.05 6.08 0.00 4.85
3053 4513 0.319083 TACGTGATGTGCCCGTTTCT 59.681 50.000 0.00 0.00 36.12 2.52
3104 4564 5.453057 GCTATCTTCATCTCAGAAGGAGCAA 60.453 44.000 18.23 0.00 44.90 3.91
3148 4608 3.066760 GCACACAAGACCAAGCTAACTTT 59.933 43.478 0.00 0.00 32.29 2.66
3201 4661 6.405538 GTCCAATCTCTTGAGTCAAAGATCT 58.594 40.000 20.92 13.37 35.67 2.75
3303 4763 1.089920 GCTTCGATCATGCAGGTGTT 58.910 50.000 0.00 0.00 0.00 3.32
3661 5220 8.601845 CAAATGATGCCAATGTTGATTGATAT 57.398 30.769 0.00 0.00 41.49 1.63
3709 5273 4.630940 AGTGCTTTCATTTGTTGTTGGTTG 59.369 37.500 0.00 0.00 0.00 3.77
3728 5292 0.323629 GGTGAATCGTTGGTGAGGGA 59.676 55.000 0.00 0.00 0.00 4.20
3922 5487 4.764679 TGTTCATTGGATTTTGGACTCG 57.235 40.909 0.00 0.00 0.00 4.18
3926 5491 2.859165 TTGGATTTTGGACTCGCTCT 57.141 45.000 0.00 0.00 0.00 4.09
3946 5511 6.109359 GCTCTCTTCAAATTAGGTCTAGCAA 58.891 40.000 0.00 0.00 0.00 3.91
3995 5561 7.191918 AGAAAATGGAATCTTTCATTACCCCT 58.808 34.615 0.00 0.00 34.60 4.79
4069 5635 4.203226 TGGTCATGCTTTATATTGCCGAA 58.797 39.130 0.00 0.00 0.00 4.30
4117 5683 8.604184 CACTAGTAGAGGACATATCTAGGGTTA 58.396 40.741 3.59 0.00 30.04 2.85
4127 5693 8.543774 GGACATATCTAGGGTTACAATCATGAT 58.456 37.037 1.18 1.18 0.00 2.45
4177 5743 3.186409 CCTATCACAAGTTCACAACACGG 59.814 47.826 0.00 0.00 0.00 4.94
4200 5766 4.890158 TCGTGTTAGCATGGGATCATAT 57.110 40.909 0.00 0.00 32.65 1.78
4285 5851 3.383761 GTGAAACAATGCTCTTGGTTGG 58.616 45.455 7.47 0.00 36.32 3.77
4290 5856 4.307032 ACAATGCTCTTGGTTGGTCTAT 57.693 40.909 4.90 0.00 0.00 1.98
4303 5869 0.107654 GGTCTATGCCCACCACTCAC 60.108 60.000 0.00 0.00 32.33 3.51
4304 5870 0.905357 GTCTATGCCCACCACTCACT 59.095 55.000 0.00 0.00 0.00 3.41
4337 5903 4.900652 AGACCATCATCTAGCTGATCTTGT 59.099 41.667 6.10 4.72 33.59 3.16
4338 5904 4.958509 ACCATCATCTAGCTGATCTTGTG 58.041 43.478 6.10 0.00 33.59 3.33
4351 5917 5.356190 GCTGATCTTGTGAGAAATGAATCCA 59.644 40.000 0.00 0.00 35.07 3.41
4387 5953 3.209097 GCCAGTGTGCCACGTGTT 61.209 61.111 15.65 0.00 39.64 3.32
4390 5956 1.095228 CCAGTGTGCCACGTGTTCTT 61.095 55.000 15.65 0.00 39.64 2.52
4391 5957 1.577468 CAGTGTGCCACGTGTTCTTA 58.423 50.000 15.65 0.00 39.64 2.10
4405 5971 7.170998 CCACGTGTTCTTAGACAGAGTAAAATT 59.829 37.037 15.65 0.00 31.12 1.82
4453 6019 3.048602 CACCGGGGTAGCGGATAG 58.951 66.667 6.32 0.00 0.00 2.08
4476 6042 9.935241 ATAGATATGTCACCTCAACATAATCAC 57.065 33.333 0.57 0.00 41.54 3.06
4480 6046 3.062639 GTCACCTCAACATAATCACGCAG 59.937 47.826 0.00 0.00 0.00 5.18
4498 6064 2.751806 GCAGAATTGCTAGTGCTTCCTT 59.248 45.455 0.00 0.00 46.95 3.36
4527 6093 3.941483 CACACTGAGTTGTCCAAGAAAGT 59.059 43.478 0.00 0.00 0.00 2.66
4531 6097 5.235186 CACTGAGTTGTCCAAGAAAGTACTG 59.765 44.000 0.00 0.00 0.00 2.74
4536 6102 6.053650 AGTTGTCCAAGAAAGTACTGTAACC 58.946 40.000 0.00 0.00 0.00 2.85
4569 6135 2.620251 AATAGCACTATTGAGCGCCA 57.380 45.000 2.29 0.00 34.71 5.69
4570 6136 2.847327 ATAGCACTATTGAGCGCCAT 57.153 45.000 2.29 0.00 34.96 4.40
4571 6137 1.869774 TAGCACTATTGAGCGCCATG 58.130 50.000 2.29 0.00 34.96 3.66
4572 6138 0.107508 AGCACTATTGAGCGCCATGT 60.108 50.000 2.29 0.00 34.96 3.21
4573 6139 1.138859 AGCACTATTGAGCGCCATGTA 59.861 47.619 2.29 0.00 34.96 2.29
4574 6140 1.261619 GCACTATTGAGCGCCATGTAC 59.738 52.381 2.29 0.00 0.00 2.90
4615 6182 1.949525 AGACATTGTCTGTTGTGTGCC 59.050 47.619 18.35 0.00 41.76 5.01
4626 6193 1.047801 TTGTGTGCCTGAGCTCTACA 58.952 50.000 16.19 11.73 40.80 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 8.475331 TCTCATAGAAAATTAGACAAACCGTC 57.525 34.615 0.00 0.00 45.77 4.79
71 72 3.194620 TGGGGCCCTATCTCACTAAAAA 58.805 45.455 25.93 0.00 0.00 1.94
72 73 2.853430 TGGGGCCCTATCTCACTAAAA 58.147 47.619 25.93 0.00 0.00 1.52
73 74 2.579624 TGGGGCCCTATCTCACTAAA 57.420 50.000 25.93 0.00 0.00 1.85
74 75 2.815357 ATGGGGCCCTATCTCACTAA 57.185 50.000 25.93 0.00 0.00 2.24
75 76 2.815357 AATGGGGCCCTATCTCACTA 57.185 50.000 22.72 0.00 0.00 2.74
76 77 1.912862 AAATGGGGCCCTATCTCACT 58.087 50.000 22.72 1.56 0.00 3.41
77 78 2.755952 AAAATGGGGCCCTATCTCAC 57.244 50.000 22.72 2.55 0.00 3.51
78 79 5.170198 ACTATAAAATGGGGCCCTATCTCA 58.830 41.667 22.72 10.99 0.00 3.27
79 80 5.780958 ACTATAAAATGGGGCCCTATCTC 57.219 43.478 22.72 4.27 0.00 2.75
80 81 6.545860 AAACTATAAAATGGGGCCCTATCT 57.454 37.500 22.72 14.12 0.00 1.98
81 82 5.414765 CGAAACTATAAAATGGGGCCCTATC 59.585 44.000 22.72 5.15 0.00 2.08
82 83 5.321927 CGAAACTATAAAATGGGGCCCTAT 58.678 41.667 25.93 20.41 0.00 2.57
83 84 4.721132 CGAAACTATAAAATGGGGCCCTA 58.279 43.478 25.93 18.54 0.00 3.53
84 85 3.562182 CGAAACTATAAAATGGGGCCCT 58.438 45.455 25.93 5.55 0.00 5.19
85 86 2.035449 GCGAAACTATAAAATGGGGCCC 59.965 50.000 18.17 18.17 0.00 5.80
86 87 2.691011 TGCGAAACTATAAAATGGGGCC 59.309 45.455 0.00 0.00 0.00 5.80
87 88 3.129638 TGTGCGAAACTATAAAATGGGGC 59.870 43.478 0.00 0.00 0.00 5.80
88 89 4.202010 CCTGTGCGAAACTATAAAATGGGG 60.202 45.833 0.00 0.00 0.00 4.96
89 90 4.202010 CCCTGTGCGAAACTATAAAATGGG 60.202 45.833 0.00 0.00 0.00 4.00
90 91 4.733523 GCCCTGTGCGAAACTATAAAATGG 60.734 45.833 0.00 0.00 0.00 3.16
91 92 4.351192 GCCCTGTGCGAAACTATAAAATG 58.649 43.478 0.00 0.00 0.00 2.32
92 93 3.380320 GGCCCTGTGCGAAACTATAAAAT 59.620 43.478 0.00 0.00 42.61 1.82
93 94 2.750712 GGCCCTGTGCGAAACTATAAAA 59.249 45.455 0.00 0.00 42.61 1.52
94 95 2.361789 GGCCCTGTGCGAAACTATAAA 58.638 47.619 0.00 0.00 42.61 1.40
95 96 1.407712 GGGCCCTGTGCGAAACTATAA 60.408 52.381 17.04 0.00 42.61 0.98
96 97 0.179468 GGGCCCTGTGCGAAACTATA 59.821 55.000 17.04 0.00 42.61 1.31
97 98 1.077716 GGGCCCTGTGCGAAACTAT 60.078 57.895 17.04 0.00 42.61 2.12
98 99 2.349755 GGGCCCTGTGCGAAACTA 59.650 61.111 17.04 0.00 42.61 2.24
101 102 3.561120 ATTCGGGCCCTGTGCGAAA 62.561 57.895 22.43 3.79 42.61 3.46
102 103 3.561120 AATTCGGGCCCTGTGCGAA 62.561 57.895 22.43 17.98 42.61 4.70
103 104 3.561120 AAATTCGGGCCCTGTGCGA 62.561 57.895 22.43 8.82 42.61 5.10
104 105 2.635443 AAAATTCGGGCCCTGTGCG 61.635 57.895 22.43 6.04 42.61 5.34
105 106 1.079888 CAAAATTCGGGCCCTGTGC 60.080 57.895 22.43 0.00 40.16 4.57
106 107 0.243636 GACAAAATTCGGGCCCTGTG 59.756 55.000 22.43 9.00 0.00 3.66
107 108 0.112412 AGACAAAATTCGGGCCCTGT 59.888 50.000 22.43 16.59 0.00 4.00
108 109 0.811281 GAGACAAAATTCGGGCCCTG 59.189 55.000 22.43 12.95 0.00 4.45
109 110 0.404040 TGAGACAAAATTCGGGCCCT 59.596 50.000 22.43 0.00 0.00 5.19
110 111 1.202348 CTTGAGACAAAATTCGGGCCC 59.798 52.381 13.57 13.57 0.00 5.80
111 112 2.159382 TCTTGAGACAAAATTCGGGCC 58.841 47.619 0.00 0.00 0.00 5.80
112 113 3.074412 TCTCTTGAGACAAAATTCGGGC 58.926 45.455 0.00 0.00 0.00 6.13
113 114 3.123621 CGTCTCTTGAGACAAAATTCGGG 59.876 47.826 24.71 6.80 38.65 5.14
114 115 3.741344 ACGTCTCTTGAGACAAAATTCGG 59.259 43.478 24.71 11.96 38.65 4.30
115 116 4.974103 ACGTCTCTTGAGACAAAATTCG 57.026 40.909 24.71 14.38 38.65 3.34
116 117 5.401674 ACGTACGTCTCTTGAGACAAAATTC 59.598 40.000 24.71 11.15 38.65 2.17
117 118 5.175126 CACGTACGTCTCTTGAGACAAAATT 59.825 40.000 19.94 8.01 38.65 1.82
118 119 4.680110 CACGTACGTCTCTTGAGACAAAAT 59.320 41.667 19.94 12.73 38.65 1.82
119 120 4.039703 CACGTACGTCTCTTGAGACAAAA 58.960 43.478 19.94 10.69 38.65 2.44
120 121 3.549423 CCACGTACGTCTCTTGAGACAAA 60.549 47.826 19.94 12.73 38.65 2.83
121 122 2.031420 CCACGTACGTCTCTTGAGACAA 60.031 50.000 19.94 13.02 38.65 3.18
122 123 1.534163 CCACGTACGTCTCTTGAGACA 59.466 52.381 19.94 8.65 38.65 3.41
123 124 1.802960 TCCACGTACGTCTCTTGAGAC 59.197 52.381 19.94 17.98 35.59 3.36
124 125 2.174363 TCCACGTACGTCTCTTGAGA 57.826 50.000 19.94 4.07 0.00 3.27
125 126 2.786854 CATCCACGTACGTCTCTTGAG 58.213 52.381 19.94 5.24 0.00 3.02
126 127 1.135489 GCATCCACGTACGTCTCTTGA 60.135 52.381 19.94 10.40 0.00 3.02
127 128 1.269166 GCATCCACGTACGTCTCTTG 58.731 55.000 19.94 14.32 0.00 3.02
128 129 0.885879 TGCATCCACGTACGTCTCTT 59.114 50.000 19.94 0.57 0.00 2.85
129 130 0.885879 TTGCATCCACGTACGTCTCT 59.114 50.000 19.94 2.36 0.00 3.10
130 131 1.654105 CTTTGCATCCACGTACGTCTC 59.346 52.381 19.94 6.45 0.00 3.36
131 132 1.671850 CCTTTGCATCCACGTACGTCT 60.672 52.381 19.94 3.17 0.00 4.18
132 133 0.719465 CCTTTGCATCCACGTACGTC 59.281 55.000 19.94 7.56 0.00 4.34
133 134 0.672401 CCCTTTGCATCCACGTACGT 60.672 55.000 16.72 16.72 0.00 3.57
134 135 0.672401 ACCCTTTGCATCCACGTACG 60.672 55.000 15.01 15.01 0.00 3.67
135 136 0.802494 CACCCTTTGCATCCACGTAC 59.198 55.000 0.00 0.00 0.00 3.67
136 137 0.687920 TCACCCTTTGCATCCACGTA 59.312 50.000 0.00 0.00 0.00 3.57
153 154 3.716195 CCACCCCGTGAGCCATCA 61.716 66.667 0.00 0.00 35.23 3.07
226 227 2.731976 GTCTGTTGCCTCGTCAAGTTAG 59.268 50.000 0.00 0.00 0.00 2.34
267 268 1.142531 GGTACTTTCGTAGCCGGGG 59.857 63.158 2.18 0.00 37.99 5.73
382 387 2.639065 GACGGTAAAATCATCTGGGCA 58.361 47.619 0.00 0.00 0.00 5.36
466 472 7.170393 AGATGTACTACTACTTGCATTGACA 57.830 36.000 0.00 0.00 0.00 3.58
565 572 2.490217 CGATTCTCCGGCGTGTCT 59.510 61.111 6.01 0.00 0.00 3.41
643 650 1.367840 GTCTGCCAACTGACGTCCT 59.632 57.895 14.12 0.00 35.41 3.85
706 717 3.876274 TTCACGAGAGATTTCTCCTGG 57.124 47.619 7.63 0.00 45.85 4.45
726 737 3.443681 CCGGAACATTGTAGCAAGGAAAT 59.556 43.478 0.00 0.00 0.00 2.17
742 753 1.153249 TCCATGAATCGGCCGGAAC 60.153 57.895 27.83 16.65 0.00 3.62
745 756 0.463654 TTTCTCCATGAATCGGCCGG 60.464 55.000 27.83 7.70 34.24 6.13
766 777 6.443206 TGGGAAAAAGATTGAGAGAGAGAGAT 59.557 38.462 0.00 0.00 0.00 2.75
775 786 5.392995 TGGACAATGGGAAAAAGATTGAGA 58.607 37.500 0.00 0.00 32.47 3.27
776 787 5.726980 TGGACAATGGGAAAAAGATTGAG 57.273 39.130 0.00 0.00 32.47 3.02
777 788 6.684897 ATTGGACAATGGGAAAAAGATTGA 57.315 33.333 0.00 0.00 32.47 2.57
778 789 8.845413 TTAATTGGACAATGGGAAAAAGATTG 57.155 30.769 0.00 0.00 33.99 2.67
782 793 8.845413 TGAATTAATTGGACAATGGGAAAAAG 57.155 30.769 5.17 0.00 0.00 2.27
818 829 7.034685 TCGAACCATAACTAATCGATGAAGA 57.965 36.000 13.44 0.00 37.59 2.87
865 884 5.190677 CCCGGTTTCATGTACTCCTAAATT 58.809 41.667 0.00 0.00 0.00 1.82
925 1114 2.547211 CGAGGACATGAATGAAGCCATC 59.453 50.000 0.00 0.00 31.40 3.51
969 1161 1.375013 GGCCCTGCAGTGCAAAATG 60.375 57.895 22.87 7.20 38.41 2.32
990 1186 0.319083 ACGTGCACATCCCGTTAGAA 59.681 50.000 18.64 0.00 0.00 2.10
1087 1283 3.940852 TCATCACGGAAATCACCAATCAG 59.059 43.478 0.00 0.00 0.00 2.90
1104 1300 5.730550 GTGTTACCACTTACCATCTCATCA 58.269 41.667 0.00 0.00 38.61 3.07
1118 1314 5.761234 TGGAACTGTATTCAAGTGTTACCAC 59.239 40.000 0.00 0.00 42.17 4.16
1160 1356 5.124936 ACTGGTCAAGTGGTCTTACAAAAAC 59.875 40.000 0.00 0.00 37.88 2.43
1177 1373 6.850752 TGATAGTAGAAACATCACTGGTCA 57.149 37.500 0.00 0.00 0.00 4.02
1200 1398 4.141733 CCAAACCAAAAACCACTCTGGATT 60.142 41.667 0.00 0.00 40.96 3.01
1240 1438 3.488489 CCCTCAACGAACGCATTAAAAG 58.512 45.455 0.00 0.00 0.00 2.27
1245 1443 2.332654 GCCCCTCAACGAACGCATT 61.333 57.895 0.00 0.00 0.00 3.56
1399 1610 9.495572 GGGATTATCTACAGGAAGAAATAACAG 57.504 37.037 0.00 0.00 0.00 3.16
1433 1644 2.472816 CCTTTTGAAACGCTGCACAAT 58.527 42.857 0.00 0.00 0.00 2.71
1456 1667 2.618794 AGCTTGATCTCCCCTAGGATG 58.381 52.381 11.48 0.45 42.93 3.51
1501 1712 0.323302 TCTTGGCGACCACAATAGCA 59.677 50.000 0.00 0.00 30.78 3.49
1523 1734 6.402226 CCCACTGTAAAGATACGCTTTTCTTC 60.402 42.308 0.00 0.00 44.24 2.87
1964 2176 8.410141 CAACAAATTTACTGACAAAGGGAGTTA 58.590 33.333 0.00 0.00 0.00 2.24
2098 2326 3.570975 AGCAGACATTGAGCACATTTTGA 59.429 39.130 0.00 0.00 0.00 2.69
2105 2333 6.197842 GCAAATTAATAGCAGACATTGAGCAC 59.802 38.462 7.68 0.00 0.00 4.40
2189 2418 6.942576 CCCGGTATCTTTGAATATGAGGAAAT 59.057 38.462 0.00 0.00 0.00 2.17
2246 2477 9.988815 AAATACAGAAGGCTTGTATAGACTATG 57.011 33.333 3.46 0.00 43.32 2.23
2377 2609 6.552008 TGTCCTGGAGAAAAAGAACCAATAT 58.448 36.000 0.00 0.00 31.85 1.28
2378 2610 5.947663 TGTCCTGGAGAAAAAGAACCAATA 58.052 37.500 0.00 0.00 31.85 1.90
2379 2611 4.803452 TGTCCTGGAGAAAAAGAACCAAT 58.197 39.130 0.00 0.00 31.85 3.16
2381 2613 3.943671 TGTCCTGGAGAAAAAGAACCA 57.056 42.857 0.00 0.00 0.00 3.67
2494 2732 6.407202 AGCAAATATCTAGTTTGTTCTCGGT 58.593 36.000 6.27 0.00 38.49 4.69
2653 2891 1.858091 ACTGATAATGCCTTCTCGCG 58.142 50.000 0.00 0.00 0.00 5.87
2749 2987 3.777106 CCTTTGCATAGGCTGAGGATA 57.223 47.619 10.46 0.00 42.01 2.59
2816 3054 4.680237 CACGCCACTGCCCTTCGA 62.680 66.667 0.00 0.00 0.00 3.71
3016 4476 1.004277 GTACTCCCTGGCCATGTTCAA 59.996 52.381 5.51 0.00 0.00 2.69
3029 4489 1.153429 GGGCACATCACGTACTCCC 60.153 63.158 0.00 0.00 0.00 4.30
3053 4513 4.326826 CCTTCCTCTTGACAATGTTGCTA 58.673 43.478 0.00 0.00 0.00 3.49
3104 4564 4.146745 GGTAATGTAACCGTCCCTCAAT 57.853 45.455 0.00 0.00 0.00 2.57
3148 4608 0.888619 CACCACGTCCTTCTGAGCTA 59.111 55.000 0.00 0.00 0.00 3.32
3201 4661 3.489355 ACATCACAGCAACAAAGATGGA 58.511 40.909 0.00 0.00 40.17 3.41
3296 4756 4.955925 TTACACTTCACACAAACACCTG 57.044 40.909 0.00 0.00 0.00 4.00
3303 4763 5.197451 AGGATTGGTTTACACTTCACACAA 58.803 37.500 0.00 0.00 0.00 3.33
3397 4953 8.024145 AGTTGGGGAAAGTCTACTTATAGATG 57.976 38.462 0.00 0.00 39.66 2.90
3402 4958 8.925338 CATAGTAGTTGGGGAAAGTCTACTTAT 58.075 37.037 8.14 0.24 40.73 1.73
3407 4963 5.278061 AGCATAGTAGTTGGGGAAAGTCTA 58.722 41.667 0.00 0.00 0.00 2.59
3549 5105 0.746063 CTTCAGGTTGTTGCCTTGCA 59.254 50.000 0.00 0.00 36.58 4.08
3661 5220 5.724328 TCACCAACACAAAAGCATTAACAA 58.276 33.333 0.00 0.00 0.00 2.83
3709 5273 0.323629 TCCCTCACCAACGATTCACC 59.676 55.000 0.00 0.00 0.00 4.02
3728 5292 8.418662 TCACTAACTAACACAACATCACTACTT 58.581 33.333 0.00 0.00 0.00 2.24
3922 5487 5.665459 TGCTAGACCTAATTTGAAGAGAGC 58.335 41.667 0.00 0.00 0.00 4.09
3926 5491 6.879458 GGAACTTGCTAGACCTAATTTGAAGA 59.121 38.462 1.04 0.00 0.00 2.87
3995 5561 8.463930 ACTCATTGTTCCATCTAAACTTTCAA 57.536 30.769 0.00 0.00 0.00 2.69
4117 5683 7.649533 AATGTGTTGTATCCATCATGATTGT 57.350 32.000 5.16 0.00 0.00 2.71
4177 5743 3.111853 TGATCCCATGCTAACACGATC 57.888 47.619 0.00 0.00 31.46 3.69
4285 5851 0.905357 AGTGAGTGGTGGGCATAGAC 59.095 55.000 0.00 0.00 0.00 2.59
4303 5869 5.999205 AGATGATGGTCTATCTAAGCCAG 57.001 43.478 0.00 0.00 35.66 4.85
4304 5870 5.420421 GCTAGATGATGGTCTATCTAAGCCA 59.580 44.000 0.00 0.00 35.96 4.75
4337 5903 6.875195 GCTTTGGAAATTGGATTCATTTCTCA 59.125 34.615 8.52 4.30 35.35 3.27
4338 5904 7.101700 AGCTTTGGAAATTGGATTCATTTCTC 58.898 34.615 8.52 2.51 35.35 2.87
4351 5917 3.068873 TGGCACGTAAAGCTTTGGAAATT 59.931 39.130 22.02 0.00 0.00 1.82
4387 5953 8.423906 AGAGGTGAATTTTACTCTGTCTAAGA 57.576 34.615 6.09 0.00 38.76 2.10
4390 5956 9.256228 ACATAGAGGTGAATTTTACTCTGTCTA 57.744 33.333 13.68 7.21 40.30 2.59
4391 5957 8.037758 CACATAGAGGTGAATTTTACTCTGTCT 58.962 37.037 13.68 5.83 41.32 3.41
4405 5971 3.982516 AGGACTAAGCACATAGAGGTGA 58.017 45.455 0.00 0.00 41.32 4.02
4439 6005 2.358267 GACATATCTATCCGCTACCCCG 59.642 54.545 0.00 0.00 0.00 5.73
4453 6019 6.346919 GCGTGATTATGTTGAGGTGACATATC 60.347 42.308 0.00 0.00 39.12 1.63
4480 6046 2.352960 CGGAAGGAAGCACTAGCAATTC 59.647 50.000 0.00 0.00 45.49 2.17
4486 6052 3.130516 TGTGTATCGGAAGGAAGCACTAG 59.869 47.826 0.00 0.00 35.62 2.57
4488 6054 1.899814 TGTGTATCGGAAGGAAGCACT 59.100 47.619 0.00 0.00 35.62 4.40
4498 6064 2.230508 GGACAACTCAGTGTGTATCGGA 59.769 50.000 0.00 0.00 0.00 4.55
4562 6128 0.804989 AAGCAAAGTACATGGCGCTC 59.195 50.000 7.64 0.00 0.00 5.03
4563 6129 1.068333 CAAAGCAAAGTACATGGCGCT 60.068 47.619 7.64 0.00 0.00 5.92
4565 6131 1.269448 ACCAAAGCAAAGTACATGGCG 59.731 47.619 0.00 0.00 0.00 5.69
4566 6132 3.506067 AGTACCAAAGCAAAGTACATGGC 59.494 43.478 0.00 0.00 39.04 4.40
4567 6133 5.240623 TCAAGTACCAAAGCAAAGTACATGG 59.759 40.000 0.00 0.00 39.04 3.66
4569 6135 6.128282 CGATCAAGTACCAAAGCAAAGTACAT 60.128 38.462 0.00 0.00 39.04 2.29
4570 6136 5.178623 CGATCAAGTACCAAAGCAAAGTACA 59.821 40.000 0.00 0.00 39.04 2.90
4571 6137 5.407387 TCGATCAAGTACCAAAGCAAAGTAC 59.593 40.000 0.00 0.00 37.27 2.73
4572 6138 5.543714 TCGATCAAGTACCAAAGCAAAGTA 58.456 37.500 0.00 0.00 0.00 2.24
4573 6139 4.385825 TCGATCAAGTACCAAAGCAAAGT 58.614 39.130 0.00 0.00 0.00 2.66
4574 6140 4.690748 TCTCGATCAAGTACCAAAGCAAAG 59.309 41.667 0.00 0.00 0.00 2.77
4615 6182 5.581126 AGAGTTGATCTTGTAGAGCTCAG 57.419 43.478 17.77 4.31 32.99 3.35
4626 6193 8.423906 TGAGTTCCTTAGTTAGAGTTGATCTT 57.576 34.615 0.00 0.00 39.64 2.40


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

AutoCloner maintained by Alex Coulton.