Multiple sequence alignment - TraesCS3A01G480400

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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 TraesCS3A01G480400 chr3A 100.000 3090 0 0 1 3090 711298528 711295439 0.000000e+00 5707.0
1 TraesCS3A01G480400 chr3A 74.947 942 185 38 1173 2085 714614906 714615825 4.830000e-103 385.0
2 TraesCS3A01G480400 chr3A 74.136 955 192 40 1164 2089 713535477 713534549 8.200000e-91 344.0
3 TraesCS3A01G480400 chr3A 100.000 28 0 0 34 61 711298374 711298347 6.000000e-03 52.8
4 TraesCS3A01G480400 chr3D 92.829 1771 91 17 958 2709 575759989 575758236 0.000000e+00 2534.0
5 TraesCS3A01G480400 chr3D 88.327 514 35 13 443 940 575760477 575759973 7.380000e-166 593.0
6 TraesCS3A01G480400 chr3D 74.628 942 188 38 1173 2085 579429346 579430265 4.870000e-98 368.0
7 TraesCS3A01G480400 chr3D 74.448 951 196 36 1159 2087 577382350 577383275 1.750000e-97 366.0
8 TraesCS3A01G480400 chr3D 73.656 949 207 33 1164 2089 577790170 577789242 8.260000e-86 327.0
9 TraesCS3A01G480400 chr3D 86.594 276 27 4 59 334 575762362 575762097 2.330000e-76 296.0
10 TraesCS3A01G480400 chr3D 73.212 937 179 47 1164 2071 577969147 577970040 1.090000e-69 274.0
11 TraesCS3A01G480400 chr3D 94.286 35 1 1 34 67 575762266 575762232 6.000000e-03 52.8
12 TraesCS3A01G480400 chr3B 93.907 1510 83 5 992 2494 768341352 768342859 0.000000e+00 2270.0
13 TraesCS3A01G480400 chr3B 95.435 1161 45 4 1101 2257 766785261 766784105 0.000000e+00 1844.0
14 TraesCS3A01G480400 chr3B 90.281 854 75 6 2240 3089 766784090 766783241 0.000000e+00 1110.0
15 TraesCS3A01G480400 chr3B 87.711 651 51 22 465 1107 766785926 766785297 0.000000e+00 732.0
16 TraesCS3A01G480400 chr3B 88.658 529 33 15 443 970 768340859 768341361 1.220000e-173 619.0
17 TraesCS3A01G480400 chr3B 74.386 937 190 37 1173 2081 773843722 773844636 3.790000e-94 355.0
18 TraesCS3A01G480400 chr3B 90.074 272 22 4 59 330 768338817 768339083 6.340000e-92 348.0
19 TraesCS3A01G480400 chr3B 74.090 934 193 39 1164 2071 771171544 771172454 3.820000e-89 339.0
20 TraesCS3A01G480400 chr3B 88.727 275 27 3 59 333 766787981 766787711 1.780000e-87 333.0
21 TraesCS3A01G480400 chr3B 73.797 935 200 34 1164 2074 770969763 770968850 8.260000e-86 327.0
22 TraesCS3A01G480400 chr3B 90.909 143 13 0 1920 2062 766659767 766659625 3.140000e-45 193.0
23 TraesCS3A01G480400 chr3B 79.399 233 43 5 59 288 111933528 111933758 3.190000e-35 159.0
24 TraesCS3A01G480400 chr3B 82.432 148 17 9 132 275 220630399 220630541 1.500000e-23 121.0
25 TraesCS3A01G480400 chr3B 82.432 148 17 9 132 275 830787126 830786984 1.500000e-23 121.0
26 TraesCS3A01G480400 chr3B 81.757 148 17 10 132 275 827412865 827413006 7.000000e-22 115.0
27 TraesCS3A01G480400 chr3B 100.000 28 0 0 34 61 768338912 768338939 6.000000e-03 52.8
28 TraesCS3A01G480400 chrUn 74.386 937 190 37 1173 2081 41302670 41303584 3.790000e-94 355.0
29 TraesCS3A01G480400 chrUn 79.602 402 60 19 2605 2997 7636576 7636964 5.080000e-68 268.0
30 TraesCS3A01G480400 chr6D 82.308 390 58 10 2614 2996 440592176 440591791 8.260000e-86 327.0
31 TraesCS3A01G480400 chr6A 81.679 393 56 14 2605 2989 506101964 506102348 2.310000e-81 313.0
32 TraesCS3A01G480400 chr6A 82.707 133 19 4 143 274 11623054 11622925 7.000000e-22 115.0
33 TraesCS3A01G480400 chr1D 80.446 404 65 13 2608 3004 436861036 436860640 2.330000e-76 296.0
34 TraesCS3A01G480400 chr1D 72.540 874 196 29 1168 2016 326909421 326908567 8.560000e-61 244.0
35 TraesCS3A01G480400 chr2D 82.424 330 48 9 2665 2989 578334648 578334972 2.350000e-71 279.0
36 TraesCS3A01G480400 chr7A 79.744 390 70 8 2609 2989 22724981 22724592 1.090000e-69 274.0
37 TraesCS3A01G480400 chr7A 80.737 353 57 9 2652 3001 18131891 18132235 6.570000e-67 265.0
38 TraesCS3A01G480400 chr7A 82.707 133 19 4 143 274 623842214 623842343 7.000000e-22 115.0
39 TraesCS3A01G480400 chr7D 80.053 376 61 11 2639 3004 162836793 162837164 1.830000e-67 267.0
40 TraesCS3A01G480400 chr1B 71.936 873 203 27 1168 2016 441386127 441385273 1.870000e-52 217.0
41 TraesCS3A01G480400 chr1A 81.879 149 18 9 132 275 555090540 555090684 1.950000e-22 117.0


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 TraesCS3A01G480400 chr3A 711295439 711298528 3089 True 2879.90 5707 100.00000 1 3090 2 chr3A.!!$R2 3089
1 TraesCS3A01G480400 chr3A 714614906 714615825 919 False 385.00 385 74.94700 1173 2085 1 chr3A.!!$F1 912
2 TraesCS3A01G480400 chr3A 713534549 713535477 928 True 344.00 344 74.13600 1164 2089 1 chr3A.!!$R1 925
3 TraesCS3A01G480400 chr3D 575758236 575762362 4126 True 868.95 2534 90.50900 34 2709 4 chr3D.!!$R2 2675
4 TraesCS3A01G480400 chr3D 579429346 579430265 919 False 368.00 368 74.62800 1173 2085 1 chr3D.!!$F3 912
5 TraesCS3A01G480400 chr3D 577382350 577383275 925 False 366.00 366 74.44800 1159 2087 1 chr3D.!!$F1 928
6 TraesCS3A01G480400 chr3D 577789242 577790170 928 True 327.00 327 73.65600 1164 2089 1 chr3D.!!$R1 925
7 TraesCS3A01G480400 chr3D 577969147 577970040 893 False 274.00 274 73.21200 1164 2071 1 chr3D.!!$F2 907
8 TraesCS3A01G480400 chr3B 766783241 766787981 4740 True 1004.75 1844 90.53850 59 3089 4 chr3B.!!$R4 3030
9 TraesCS3A01G480400 chr3B 768338817 768342859 4042 False 822.45 2270 93.15975 34 2494 4 chr3B.!!$F6 2460
10 TraesCS3A01G480400 chr3B 773843722 773844636 914 False 355.00 355 74.38600 1173 2081 1 chr3B.!!$F4 908
11 TraesCS3A01G480400 chr3B 771171544 771172454 910 False 339.00 339 74.09000 1164 2071 1 chr3B.!!$F3 907
12 TraesCS3A01G480400 chr3B 770968850 770969763 913 True 327.00 327 73.79700 1164 2074 1 chr3B.!!$R2 910
13 TraesCS3A01G480400 chrUn 41302670 41303584 914 False 355.00 355 74.38600 1173 2081 1 chrUn.!!$F2 908
14 TraesCS3A01G480400 chr1D 326908567 326909421 854 True 244.00 244 72.54000 1168 2016 1 chr1D.!!$R1 848
15 TraesCS3A01G480400 chr1B 441385273 441386127 854 True 217.00 217 71.93600 1168 2016 1 chr1B.!!$R1 848

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
936 3204 0.179171 CGTACGTACCAGGTGCAGAG 60.179 60.0 19.67 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 4861 0.105039 CTCTATTGCCAGGACGTCCC 59.895 60.0 30.82 16.33 36.42 4.46 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
26 27 8.827177 AAAAGTCGTGATGTATTTCACTTAGA 57.173 30.769 3.41 0.00 43.10 2.10
27 28 8.827177 AAAGTCGTGATGTATTTCACTTAGAA 57.173 30.769 3.41 0.00 43.10 2.10
44 45 9.990360 TCACTTAGAAATTGTACTCAACATACA 57.010 29.630 0.00 0.00 38.10 2.29
46 47 9.216117 ACTTAGAAATTGTACTCAACATACACC 57.784 33.333 0.00 0.00 38.10 4.16
47 48 9.214957 CTTAGAAATTGTACTCAACATACACCA 57.785 33.333 0.00 0.00 38.10 4.17
48 49 9.733556 TTAGAAATTGTACTCAACATACACCAT 57.266 29.630 0.00 0.00 38.10 3.55
49 50 8.635765 AGAAATTGTACTCAACATACACCATT 57.364 30.769 0.00 0.00 38.10 3.16
50 51 9.733556 AGAAATTGTACTCAACATACACCATTA 57.266 29.630 0.00 0.00 38.10 1.90
51 52 9.769093 GAAATTGTACTCAACATACACCATTAC 57.231 33.333 0.00 0.00 38.10 1.89
52 53 8.856153 AATTGTACTCAACATACACCATTACA 57.144 30.769 0.00 0.00 38.10 2.41
53 54 9.461312 AATTGTACTCAACATACACCATTACAT 57.539 29.630 0.00 0.00 38.10 2.29
54 55 7.841915 TGTACTCAACATACACCATTACATG 57.158 36.000 0.00 0.00 31.43 3.21
55 56 7.390823 TGTACTCAACATACACCATTACATGT 58.609 34.615 2.69 2.69 31.43 3.21
56 57 8.532819 TGTACTCAACATACACCATTACATGTA 58.467 33.333 0.08 0.08 35.82 2.29
57 58 9.542462 GTACTCAACATACACCATTACATGTAT 57.458 33.333 6.36 0.00 41.63 2.29
72 73 4.796606 ACATGTATCATCTTTGGGGAAGG 58.203 43.478 0.00 0.00 35.98 3.46
249 250 4.986659 CCATTAAATGCATTGCTAGGCTTC 59.013 41.667 13.82 0.00 30.95 3.86
258 259 6.298361 TGCATTGCTAGGCTTCTAATTGATA 58.702 36.000 10.49 0.00 30.95 2.15
264 265 9.845740 TTGCTAGGCTTCTAATTGATACAATTA 57.154 29.630 13.69 13.69 0.00 1.40
293 294 8.542497 TTTGAACAGTAGGTACATGACATAAC 57.458 34.615 0.00 0.00 0.00 1.89
304 305 6.764560 GGTACATGACATAACCGTTAGGAATT 59.235 38.462 9.82 0.00 41.02 2.17
359 2365 4.497473 TTTCTAAAACAGCGGACCATTG 57.503 40.909 0.00 0.00 0.00 2.82
395 2401 3.000773 CAGCACAAAAAGAAAACAGCGTC 60.001 43.478 0.00 0.00 0.00 5.19
440 2446 4.725758 CGAACAGCGCAAACTAGC 57.274 55.556 11.47 0.00 0.00 3.42
499 2748 4.220602 GTCCATGCTTCCAAAACCATTACT 59.779 41.667 0.00 0.00 0.00 2.24
506 2755 6.491745 TGCTTCCAAAACCATTACTATCAACA 59.508 34.615 0.00 0.00 0.00 3.33
507 2756 7.178274 TGCTTCCAAAACCATTACTATCAACAT 59.822 33.333 0.00 0.00 0.00 2.71
509 2758 9.573133 CTTCCAAAACCATTACTATCAACATTC 57.427 33.333 0.00 0.00 0.00 2.67
510 2759 8.642935 TCCAAAACCATTACTATCAACATTCA 57.357 30.769 0.00 0.00 0.00 2.57
512 2761 9.139174 CCAAAACCATTACTATCAACATTCAAC 57.861 33.333 0.00 0.00 0.00 3.18
513 2762 9.689976 CAAAACCATTACTATCAACATTCAACA 57.310 29.630 0.00 0.00 0.00 3.33
514 2763 9.912634 AAAACCATTACTATCAACATTCAACAG 57.087 29.630 0.00 0.00 0.00 3.16
555 2804 4.624452 GTCCAGTCAAAAGGATGTACGTAC 59.376 45.833 18.90 18.90 36.11 3.67
618 2869 1.832167 GCTGTTTCCCCCAAGTGCA 60.832 57.895 0.00 0.00 0.00 4.57
689 2940 2.589890 GTAGCTTACGGGCGATGTG 58.410 57.895 0.00 0.00 37.29 3.21
693 2944 1.296056 GCTTACGGGCGATGTGTTGT 61.296 55.000 0.00 0.00 0.00 3.32
738 2990 2.797087 CGCGTATTCCATTCCACGTACT 60.797 50.000 0.00 0.00 36.78 2.73
795 3061 2.034221 GGAAAACGGGAGCTGGCT 59.966 61.111 0.00 0.00 0.00 4.75
796 3062 1.298667 GGAAAACGGGAGCTGGCTA 59.701 57.895 0.00 0.00 0.00 3.93
797 3063 0.744771 GGAAAACGGGAGCTGGCTAG 60.745 60.000 0.00 0.00 0.00 3.42
853 3119 7.361286 GCCTAATTACATTACATCCTAGCTTGC 60.361 40.741 0.00 0.00 0.00 4.01
859 3125 2.185004 ACATCCTAGCTTGCGTTGTT 57.815 45.000 0.00 0.00 0.00 2.83
881 3149 4.901868 TCGTATAAATAGGGGGTGAATGC 58.098 43.478 0.00 0.00 0.00 3.56
901 3169 3.808726 TGCTTGGTTCATTTCATGCAAAC 59.191 39.130 0.00 0.00 39.80 2.93
903 3171 3.023946 TGGTTCATTTCATGCAAACCG 57.976 42.857 9.12 0.00 39.01 4.44
913 3181 4.003011 GCAAACCGCACGCACGTA 62.003 61.111 0.00 0.00 41.79 3.57
914 3182 2.127906 CAAACCGCACGCACGTAC 60.128 61.111 0.00 0.00 0.00 3.67
915 3183 3.694394 AAACCGCACGCACGTACG 61.694 61.111 15.01 15.01 34.93 3.67
931 3199 4.751539 CGACGTACGTACCAGGTG 57.248 61.111 22.87 7.97 37.22 4.00
932 3200 1.512734 CGACGTACGTACCAGGTGC 60.513 63.158 22.87 5.09 37.22 5.01
933 3201 1.580942 GACGTACGTACCAGGTGCA 59.419 57.895 22.87 0.00 0.00 4.57
934 3202 0.455633 GACGTACGTACCAGGTGCAG 60.456 60.000 22.87 5.85 0.00 4.41
935 3203 0.890542 ACGTACGTACCAGGTGCAGA 60.891 55.000 21.41 0.00 0.00 4.26
936 3204 0.179171 CGTACGTACCAGGTGCAGAG 60.179 60.000 19.67 0.00 0.00 3.35
937 3205 0.886563 GTACGTACCAGGTGCAGAGT 59.113 55.000 15.00 0.39 0.00 3.24
938 3206 1.271656 GTACGTACCAGGTGCAGAGTT 59.728 52.381 15.00 0.00 0.00 3.01
939 3207 0.756903 ACGTACCAGGTGCAGAGTTT 59.243 50.000 8.59 0.00 0.00 2.66
940 3208 1.140252 ACGTACCAGGTGCAGAGTTTT 59.860 47.619 8.59 0.00 0.00 2.43
941 3209 1.531149 CGTACCAGGTGCAGAGTTTTG 59.469 52.381 8.59 0.00 0.00 2.44
942 3210 1.880027 GTACCAGGTGCAGAGTTTTGG 59.120 52.381 0.76 0.00 0.00 3.28
943 3211 0.550914 ACCAGGTGCAGAGTTTTGGA 59.449 50.000 0.00 0.00 0.00 3.53
944 3212 1.064017 ACCAGGTGCAGAGTTTTGGAA 60.064 47.619 0.00 0.00 0.00 3.53
945 3213 1.610522 CCAGGTGCAGAGTTTTGGAAG 59.389 52.381 0.00 0.00 0.00 3.46
946 3214 2.575532 CAGGTGCAGAGTTTTGGAAGA 58.424 47.619 0.00 0.00 0.00 2.87
947 3215 3.152341 CAGGTGCAGAGTTTTGGAAGAT 58.848 45.455 0.00 0.00 0.00 2.40
948 3216 3.190118 CAGGTGCAGAGTTTTGGAAGATC 59.810 47.826 0.00 0.00 0.00 2.75
949 3217 3.073650 AGGTGCAGAGTTTTGGAAGATCT 59.926 43.478 0.00 0.00 0.00 2.75
950 3218 4.287067 AGGTGCAGAGTTTTGGAAGATCTA 59.713 41.667 0.00 0.00 0.00 1.98
951 3219 4.633565 GGTGCAGAGTTTTGGAAGATCTAG 59.366 45.833 0.00 0.00 0.00 2.43
952 3220 4.094146 GTGCAGAGTTTTGGAAGATCTAGC 59.906 45.833 0.00 0.00 0.00 3.42
953 3221 4.019860 TGCAGAGTTTTGGAAGATCTAGCT 60.020 41.667 0.00 0.00 0.00 3.32
954 3222 4.332268 GCAGAGTTTTGGAAGATCTAGCTG 59.668 45.833 0.00 0.00 0.00 4.24
955 3223 4.332268 CAGAGTTTTGGAAGATCTAGCTGC 59.668 45.833 0.00 0.00 0.00 5.25
956 3224 4.019860 AGAGTTTTGGAAGATCTAGCTGCA 60.020 41.667 1.02 0.00 0.00 4.41
1077 3389 2.496291 GGCATCCATTCCTGCAGGC 61.496 63.158 28.91 13.21 40.18 4.85
1147 3502 0.875040 TTCGGTTGCGCGTTTCACTA 60.875 50.000 8.43 0.00 0.00 2.74
2074 4460 1.885850 GGACAAATCGCCGGCGTAT 60.886 57.895 44.16 32.38 40.74 3.06
2105 4492 0.105039 CTAGAAGGCGGGACACATCC 59.895 60.000 0.00 0.00 45.42 3.51
2181 4570 2.000447 CTACTGCGGGCTTTGTACTTC 59.000 52.381 0.00 0.00 0.00 3.01
2182 4571 0.605589 ACTGCGGGCTTTGTACTTCC 60.606 55.000 0.00 0.00 0.00 3.46
2183 4572 0.321653 CTGCGGGCTTTGTACTTCCT 60.322 55.000 0.00 0.00 0.00 3.36
2184 4573 0.109723 TGCGGGCTTTGTACTTCCTT 59.890 50.000 0.00 0.00 0.00 3.36
2229 4622 0.986992 GCGAACATCATGCTTTGCAC 59.013 50.000 7.10 0.00 43.04 4.57
2230 4623 1.621107 CGAACATCATGCTTTGCACC 58.379 50.000 0.00 0.00 43.04 5.01
2236 4629 0.608856 TCATGCTTTGCACCGATGGT 60.609 50.000 0.00 0.00 43.04 3.55
2280 4705 2.314561 TGACGAAAGCGCTCAAATTG 57.685 45.000 12.06 4.20 42.48 2.32
2309 4737 3.440522 GGAGACAAACAATAAGAGGCACC 59.559 47.826 0.00 0.00 0.00 5.01
2343 4771 6.486993 ACTGTGATCTTTCTTTTACCACTTCC 59.513 38.462 0.00 0.00 0.00 3.46
2349 4777 6.659824 TCTTTCTTTTACCACTTCCTTCTGT 58.340 36.000 0.00 0.00 0.00 3.41
2452 4885 0.105039 GGGACGTCCTGGCAATAGAG 59.895 60.000 32.52 0.00 35.95 2.43
2475 4908 2.559668 ACTCCCACATGCAACATTTCTG 59.440 45.455 0.00 0.00 0.00 3.02
2518 4951 8.568676 TTTTATTTCCGTGGTGATTCTAATCA 57.431 30.769 1.23 1.23 42.78 2.57
2544 4977 7.483307 AGGTATATCGTTATGTGTGTACGTTT 58.517 34.615 0.00 0.00 36.70 3.60
2620 5054 1.544724 GAGCATCTCTAGCCGATCCT 58.455 55.000 0.00 0.00 0.00 3.24
2621 5055 1.472480 GAGCATCTCTAGCCGATCCTC 59.528 57.143 0.00 0.00 0.00 3.71
2631 5066 3.634397 AGCCGATCCTCAAAAATGAGA 57.366 42.857 7.39 0.00 38.13 3.27
2638 5073 6.989169 CCGATCCTCAAAAATGAGAAGTATCT 59.011 38.462 7.39 0.00 38.13 1.98
2643 5078 4.635765 TCAAAAATGAGAAGTATCTGGCCG 59.364 41.667 0.00 0.00 35.54 6.13
2645 5080 3.742433 AATGAGAAGTATCTGGCCGAG 57.258 47.619 0.00 0.00 35.54 4.63
2655 5090 1.103803 TCTGGCCGAGTAAGCTAGTG 58.896 55.000 0.00 0.00 39.62 2.74
2663 5098 4.083377 GCCGAGTAAGCTAGTGGAGTATAC 60.083 50.000 0.00 0.00 0.00 1.47
2688 5124 8.537858 ACTACTCCACTAAATTTTAATCGGACT 58.462 33.333 0.00 0.00 0.00 3.85
2711 5148 4.184649 AGCCCATCCCCTAAATAAACAG 57.815 45.455 0.00 0.00 0.00 3.16
2752 5189 5.802465 TCATTTGCATTTCATTTTAGGCCA 58.198 33.333 5.01 0.00 0.00 5.36
2761 5198 5.452078 TTCATTTTAGGCCACTGAAACAG 57.548 39.130 5.01 0.00 35.38 3.16
2766 5203 7.450014 TCATTTTAGGCCACTGAAACAGATTTA 59.550 33.333 5.01 0.00 35.38 1.40
2851 5288 4.278858 TCGCAACGAGAACAAAATCAAAG 58.721 39.130 0.00 0.00 0.00 2.77
2895 5332 8.894768 AGACACTTTAATACATATCCAGCTTC 57.105 34.615 0.00 0.00 0.00 3.86
2906 5343 2.698855 TCCAGCTTCCATAACTGCTC 57.301 50.000 0.00 0.00 33.03 4.26
2960 5397 7.174946 GTCTTCACTGTTAATTCCCTCAATTGA 59.825 37.037 8.12 8.12 35.34 2.57
2962 5399 6.303054 TCACTGTTAATTCCCTCAATTGACA 58.697 36.000 3.38 0.00 44.57 3.58
2963 5400 6.775142 TCACTGTTAATTCCCTCAATTGACAA 59.225 34.615 3.38 0.00 45.47 3.18
2977 5414 1.215014 TGACAACTCGAGCTTGCACG 61.215 55.000 13.61 6.12 0.00 5.34
2981 5418 0.319555 AACTCGAGCTTGCACGCTTA 60.320 50.000 19.70 9.79 41.08 3.09
2989 5426 2.162408 AGCTTGCACGCTTATTTCTTCC 59.838 45.455 12.63 0.00 36.74 3.46
3000 5437 4.330347 GCTTATTTCTTCCTCAGTTCCGAC 59.670 45.833 0.00 0.00 0.00 4.79
3014 5451 4.461992 GTTCCGACGAACAAAAAGATGA 57.538 40.909 0.00 0.00 46.49 2.92
3030 5467 7.622893 AAAAGATGAGCTCAAGAATAAGGAC 57.377 36.000 22.50 2.68 0.00 3.85
3031 5468 5.946942 AGATGAGCTCAAGAATAAGGACA 57.053 39.130 22.50 0.00 0.00 4.02
3034 5471 4.825422 TGAGCTCAAGAATAAGGACACAG 58.175 43.478 15.67 0.00 0.00 3.66
3046 5483 7.557719 AGAATAAGGACACAGTGATAAAATGGG 59.442 37.037 7.81 0.00 0.00 4.00
3065 5502 2.291540 GGGACAAGGAATTGGTGATGGA 60.292 50.000 0.00 0.00 0.00 3.41
3068 5505 2.102578 CAAGGAATTGGTGATGGACCC 58.897 52.381 0.00 0.00 45.45 4.46
3077 5514 2.041081 TGGTGATGGACCCAACCTAAAG 59.959 50.000 10.34 0.00 45.45 1.85
3081 5518 3.849574 TGATGGACCCAACCTAAAGATCA 59.150 43.478 0.00 0.00 0.00 2.92
3089 5526 7.614192 GGACCCAACCTAAAGATCATAAAAGAA 59.386 37.037 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.990360 TGTATGTTGAGTACAATTTCTAAGTGA 57.010 29.630 0.00 0.00 40.89 3.41
20 21 9.216117 GGTGTATGTTGAGTACAATTTCTAAGT 57.784 33.333 0.00 0.00 40.89 2.24
21 22 9.214957 TGGTGTATGTTGAGTACAATTTCTAAG 57.785 33.333 0.00 0.00 40.89 2.18
22 23 9.733556 ATGGTGTATGTTGAGTACAATTTCTAA 57.266 29.630 0.00 0.00 40.89 2.10
23 24 9.733556 AATGGTGTATGTTGAGTACAATTTCTA 57.266 29.630 0.00 0.00 40.89 2.10
24 25 8.635765 AATGGTGTATGTTGAGTACAATTTCT 57.364 30.769 0.00 0.00 40.89 2.52
25 26 9.769093 GTAATGGTGTATGTTGAGTACAATTTC 57.231 33.333 0.00 0.00 40.89 2.17
26 27 9.290988 TGTAATGGTGTATGTTGAGTACAATTT 57.709 29.630 0.00 0.00 40.89 1.82
27 28 8.856153 TGTAATGGTGTATGTTGAGTACAATT 57.144 30.769 0.00 0.00 40.89 2.32
28 29 8.892723 CATGTAATGGTGTATGTTGAGTACAAT 58.107 33.333 0.00 0.00 41.79 2.71
29 30 8.262715 CATGTAATGGTGTATGTTGAGTACAA 57.737 34.615 0.00 0.00 41.79 2.41
30 31 7.841915 CATGTAATGGTGTATGTTGAGTACA 57.158 36.000 0.00 0.00 41.79 2.90
45 46 7.040201 CTTCCCCAAAGATGATACATGTAATGG 60.040 40.741 10.14 9.33 42.73 3.16
46 47 7.040201 CCTTCCCCAAAGATGATACATGTAATG 60.040 40.741 10.14 1.37 43.56 1.90
47 48 7.006509 CCTTCCCCAAAGATGATACATGTAAT 58.993 38.462 10.14 0.00 37.12 1.89
48 49 6.159575 TCCTTCCCCAAAGATGATACATGTAA 59.840 38.462 10.14 0.00 37.12 2.41
49 50 5.669904 TCCTTCCCCAAAGATGATACATGTA 59.330 40.000 8.27 8.27 37.12 2.29
50 51 4.478317 TCCTTCCCCAAAGATGATACATGT 59.522 41.667 2.69 2.69 37.12 3.21
51 52 5.052693 TCCTTCCCCAAAGATGATACATG 57.947 43.478 0.00 0.00 37.12 3.21
52 53 5.194537 AGTTCCTTCCCCAAAGATGATACAT 59.805 40.000 0.00 0.00 37.12 2.29
53 54 4.540099 AGTTCCTTCCCCAAAGATGATACA 59.460 41.667 0.00 0.00 37.12 2.29
54 55 5.117406 AGTTCCTTCCCCAAAGATGATAC 57.883 43.478 0.00 0.00 37.12 2.24
55 56 5.369699 CCTAGTTCCTTCCCCAAAGATGATA 59.630 44.000 0.00 0.00 37.12 2.15
56 57 4.166919 CCTAGTTCCTTCCCCAAAGATGAT 59.833 45.833 0.00 0.00 37.12 2.45
57 58 3.523564 CCTAGTTCCTTCCCCAAAGATGA 59.476 47.826 0.00 0.00 37.12 2.92
72 73 5.805728 TCATTCCCTCTTGAAACCTAGTTC 58.194 41.667 0.00 0.00 0.00 3.01
123 124 1.140052 TCTCAAGTCCAACTGGCGAAA 59.860 47.619 0.00 0.00 34.44 3.46
130 131 5.652014 TGTGAAAACAATCTCAAGTCCAACT 59.348 36.000 0.00 0.00 0.00 3.16
189 190 3.647590 ACAGACCCAAGAAATTGCCAATT 59.352 39.130 0.00 0.00 0.00 2.32
192 193 2.380064 ACAGACCCAAGAAATTGCCA 57.620 45.000 0.00 0.00 0.00 4.92
194 195 2.802247 GCAAACAGACCCAAGAAATTGC 59.198 45.455 0.00 0.00 35.69 3.56
195 196 4.326504 AGCAAACAGACCCAAGAAATTG 57.673 40.909 0.00 0.00 0.00 2.32
196 197 7.961326 ATATAGCAAACAGACCCAAGAAATT 57.039 32.000 0.00 0.00 0.00 1.82
201 202 7.196331 GCTTAAATATAGCAAACAGACCCAAG 58.804 38.462 0.00 0.00 38.51 3.61
264 265 8.458573 TGTCATGTACCTACTGTTCAAATTTT 57.541 30.769 0.00 0.00 0.00 1.82
275 276 5.927281 AACGGTTATGTCATGTACCTACT 57.073 39.130 13.83 0.71 0.00 2.57
276 277 6.039717 TCCTAACGGTTATGTCATGTACCTAC 59.960 42.308 13.83 0.00 0.00 3.18
340 2346 2.432444 CCAATGGTCCGCTGTTTTAGA 58.568 47.619 0.00 0.00 0.00 2.10
341 2347 1.135402 GCCAATGGTCCGCTGTTTTAG 60.135 52.381 0.00 0.00 0.00 1.85
368 2374 6.142139 GCTGTTTTCTTTTTGTGCTGTTTTT 58.858 32.000 0.00 0.00 0.00 1.94
372 2378 2.923020 CGCTGTTTTCTTTTTGTGCTGT 59.077 40.909 0.00 0.00 0.00 4.40
373 2379 2.923020 ACGCTGTTTTCTTTTTGTGCTG 59.077 40.909 0.00 0.00 0.00 4.41
376 2382 3.506810 TGGACGCTGTTTTCTTTTTGTG 58.493 40.909 0.00 0.00 0.00 3.33
377 2383 3.769536 CTGGACGCTGTTTTCTTTTTGT 58.230 40.909 0.00 0.00 0.00 2.83
378 2384 2.535574 GCTGGACGCTGTTTTCTTTTTG 59.464 45.455 0.00 0.00 35.14 2.44
440 2446 1.411089 CGCGAACCGAAGAAGAACG 59.589 57.895 0.00 0.00 40.02 3.95
499 2748 7.148255 GGCATGTTCTACTGTTGAATGTTGATA 60.148 37.037 7.87 0.00 0.00 2.15
506 2755 5.072741 AGTTGGCATGTTCTACTGTTGAAT 58.927 37.500 7.87 0.00 0.00 2.57
507 2756 4.460263 AGTTGGCATGTTCTACTGTTGAA 58.540 39.130 0.53 0.53 0.00 2.69
509 2758 5.470098 ACTTAGTTGGCATGTTCTACTGTTG 59.530 40.000 12.53 0.00 0.00 3.33
510 2759 5.621193 ACTTAGTTGGCATGTTCTACTGTT 58.379 37.500 12.53 0.00 0.00 3.16
512 2761 4.631813 GGACTTAGTTGGCATGTTCTACTG 59.368 45.833 12.53 3.63 0.00 2.74
513 2762 4.286032 TGGACTTAGTTGGCATGTTCTACT 59.714 41.667 0.00 2.87 0.00 2.57
514 2763 4.575885 TGGACTTAGTTGGCATGTTCTAC 58.424 43.478 0.00 0.00 0.00 2.59
555 2804 3.555956 GGAATTCCAGTGTACGTAGCATG 59.444 47.826 20.04 0.00 35.64 4.06
594 2844 2.991540 GGGGGAAACAGCTGTGCC 60.992 66.667 22.49 23.42 0.00 5.01
689 2940 0.949105 ACGATCTGGTTCGGCACAAC 60.949 55.000 0.00 0.00 43.33 3.32
693 2944 1.080093 GTCACGATCTGGTTCGGCA 60.080 57.895 0.00 0.00 43.33 5.69
738 2990 1.203994 GTAGACGTTTGCTCTGGCCTA 59.796 52.381 3.32 0.00 37.74 3.93
817 3083 5.736951 AATGTAATTAGGCAGTTTGGCAA 57.263 34.783 0.00 0.00 46.46 4.52
859 3125 4.595781 AGCATTCACCCCCTATTTATACGA 59.404 41.667 0.00 0.00 0.00 3.43
914 3182 1.512734 GCACCTGGTACGTACGTCG 60.513 63.158 26.53 11.64 46.00 5.12
915 3183 0.455633 CTGCACCTGGTACGTACGTC 60.456 60.000 26.53 15.93 0.00 4.34
927 3195 3.073650 AGATCTTCCAAAACTCTGCACCT 59.926 43.478 0.00 0.00 0.00 4.00
928 3196 3.416156 AGATCTTCCAAAACTCTGCACC 58.584 45.455 0.00 0.00 0.00 5.01
929 3197 4.094146 GCTAGATCTTCCAAAACTCTGCAC 59.906 45.833 0.00 0.00 0.00 4.57
930 3198 4.019860 AGCTAGATCTTCCAAAACTCTGCA 60.020 41.667 0.00 0.00 0.00 4.41
931 3199 4.332268 CAGCTAGATCTTCCAAAACTCTGC 59.668 45.833 0.00 0.00 0.00 4.26
932 3200 4.332268 GCAGCTAGATCTTCCAAAACTCTG 59.668 45.833 0.00 0.00 0.00 3.35
933 3201 4.019860 TGCAGCTAGATCTTCCAAAACTCT 60.020 41.667 0.00 0.00 0.00 3.24
934 3202 4.094146 GTGCAGCTAGATCTTCCAAAACTC 59.906 45.833 0.00 0.00 0.00 3.01
935 3203 4.006319 GTGCAGCTAGATCTTCCAAAACT 58.994 43.478 0.00 0.00 0.00 2.66
936 3204 4.006319 AGTGCAGCTAGATCTTCCAAAAC 58.994 43.478 0.00 0.00 0.00 2.43
937 3205 4.292186 AGTGCAGCTAGATCTTCCAAAA 57.708 40.909 0.00 0.00 0.00 2.44
938 3206 3.988976 AGTGCAGCTAGATCTTCCAAA 57.011 42.857 0.00 0.00 0.00 3.28
939 3207 4.026744 AGTAGTGCAGCTAGATCTTCCAA 58.973 43.478 0.00 0.00 0.00 3.53
940 3208 3.382865 CAGTAGTGCAGCTAGATCTTCCA 59.617 47.826 0.00 0.00 0.00 3.53
941 3209 3.243704 CCAGTAGTGCAGCTAGATCTTCC 60.244 52.174 0.00 0.00 0.00 3.46
942 3210 3.383185 ACCAGTAGTGCAGCTAGATCTTC 59.617 47.826 0.00 0.00 0.00 2.87
943 3211 3.131933 CACCAGTAGTGCAGCTAGATCTT 59.868 47.826 0.00 0.00 40.28 2.40
944 3212 2.692557 CACCAGTAGTGCAGCTAGATCT 59.307 50.000 0.00 0.00 40.28 2.75
945 3213 3.090952 CACCAGTAGTGCAGCTAGATC 57.909 52.381 0.00 0.00 40.28 2.75
956 3224 1.768870 ACCAAACTCTGCACCAGTAGT 59.231 47.619 0.00 0.00 32.61 2.73
981 3255 3.315749 CCATCTCCACTAGTACGTCTTCC 59.684 52.174 0.00 0.00 0.00 3.46
1147 3502 2.624838 CTGCACCTCTGTGTTTTCCAAT 59.375 45.455 0.00 0.00 44.65 3.16
1581 3946 3.953652 TGCCTTGGGAGGGAGGGA 61.954 66.667 0.00 0.00 43.75 4.20
1764 4141 1.666872 AGGTTCTGGTACGCGTTGC 60.667 57.895 20.78 11.35 0.00 4.17
2074 4460 2.168521 CGCCTTCTAGAAACTGATGGGA 59.831 50.000 6.63 0.00 0.00 4.37
2181 4570 4.125703 CAGTAGAGGCAGCTTATTCAAGG 58.874 47.826 0.00 0.00 31.96 3.61
2182 4571 4.764172 ACAGTAGAGGCAGCTTATTCAAG 58.236 43.478 0.00 0.00 34.66 3.02
2183 4572 4.826274 ACAGTAGAGGCAGCTTATTCAA 57.174 40.909 0.00 0.00 0.00 2.69
2184 4573 5.201243 TCTACAGTAGAGGCAGCTTATTCA 58.799 41.667 6.15 0.00 0.00 2.57
2229 4622 2.868253 GGACCTTTTCCACCATCGG 58.132 57.895 0.00 0.00 45.10 4.18
2280 4705 7.295930 CCTCTTATTGTTTGTCTCCGTTAAAC 58.704 38.462 0.00 0.00 35.46 2.01
2309 4737 4.521146 AGAAAGATCACAGTATTGCCAGG 58.479 43.478 0.00 0.00 0.00 4.45
2343 4771 0.457851 CACCTAGGGCTCGACAGAAG 59.542 60.000 14.81 0.00 0.00 2.85
2433 4861 0.105039 CTCTATTGCCAGGACGTCCC 59.895 60.000 30.82 16.33 36.42 4.46
2452 4885 3.256631 AGAAATGTTGCATGTGGGAGTTC 59.743 43.478 0.00 0.00 0.00 3.01
2485 4918 2.920490 CCACGGAAATAAAATGTTGCCG 59.080 45.455 4.88 4.88 42.64 5.69
2518 4951 7.031226 ACGTACACACATAACGATATACCTT 57.969 36.000 0.63 0.00 39.80 3.50
2620 5054 4.635765 CGGCCAGATACTTCTCATTTTTGA 59.364 41.667 2.24 0.00 0.00 2.69
2621 5055 4.635765 TCGGCCAGATACTTCTCATTTTTG 59.364 41.667 2.24 0.00 0.00 2.44
2631 5066 2.389715 AGCTTACTCGGCCAGATACTT 58.610 47.619 2.24 0.00 0.00 2.24
2638 5073 0.323999 TCCACTAGCTTACTCGGCCA 60.324 55.000 2.24 0.00 0.00 5.36
2663 5098 8.943909 AGTCCGATTAAAATTTAGTGGAGTAG 57.056 34.615 7.90 0.00 0.00 2.57
2675 5111 5.070685 GGATGGGCTAAGTCCGATTAAAAT 58.929 41.667 0.00 0.00 0.00 1.82
2680 5116 0.765510 GGGATGGGCTAAGTCCGATT 59.234 55.000 0.00 0.00 32.71 3.34
2688 5124 5.433712 TCTGTTTATTTAGGGGATGGGCTAA 59.566 40.000 0.00 0.00 0.00 3.09
2747 5184 5.567423 GCAATTAAATCTGTTTCAGTGGCCT 60.567 40.000 3.32 0.00 32.61 5.19
2805 5242 6.121776 ACAGTTGGTGAATTATGTACTCCA 57.878 37.500 0.00 0.00 0.00 3.86
2842 5279 8.614469 TTGTGGTTCTTGTTTTCTTTGATTTT 57.386 26.923 0.00 0.00 0.00 1.82
2851 5288 7.480810 AGTGTCTAATTGTGGTTCTTGTTTTC 58.519 34.615 0.00 0.00 0.00 2.29
2891 5328 2.409948 AGTGGAGCAGTTATGGAAGC 57.590 50.000 0.00 0.00 0.00 3.86
2892 5329 4.744795 ACTAGTGGAGCAGTTATGGAAG 57.255 45.455 0.00 0.00 0.00 3.46
2929 5366 7.180229 TGAGGGAATTAACAGTGAAGACATAGA 59.820 37.037 0.00 0.00 0.00 1.98
2941 5378 7.219484 AGTTGTCAATTGAGGGAATTAACAG 57.781 36.000 8.80 0.00 34.29 3.16
2960 5397 2.598632 GCGTGCAAGCTCGAGTTGT 61.599 57.895 17.84 0.00 35.30 3.32
2962 5399 2.029666 AGCGTGCAAGCTCGAGTT 59.970 55.556 21.99 4.78 45.67 3.01
2977 5414 4.330347 GTCGGAACTGAGGAAGAAATAAGC 59.670 45.833 0.00 0.00 0.00 3.09
2981 5418 2.561419 TCGTCGGAACTGAGGAAGAAAT 59.439 45.455 3.96 0.00 30.45 2.17
3000 5437 5.348418 TCTTGAGCTCATCTTTTTGTTCG 57.652 39.130 19.04 0.00 0.00 3.95
3009 5446 5.188555 TGTGTCCTTATTCTTGAGCTCATCT 59.811 40.000 19.04 5.22 0.00 2.90
3012 5449 4.284490 ACTGTGTCCTTATTCTTGAGCTCA 59.716 41.667 13.74 13.74 0.00 4.26
3014 5451 4.284490 TCACTGTGTCCTTATTCTTGAGCT 59.716 41.667 7.79 0.00 0.00 4.09
3030 5467 5.009631 TCCTTGTCCCATTTTATCACTGTG 58.990 41.667 0.17 0.17 0.00 3.66
3031 5468 5.255397 TCCTTGTCCCATTTTATCACTGT 57.745 39.130 0.00 0.00 0.00 3.55
3034 5471 6.070824 ACCAATTCCTTGTCCCATTTTATCAC 60.071 38.462 0.00 0.00 0.00 3.06
3046 5483 2.755103 GGTCCATCACCAATTCCTTGTC 59.245 50.000 0.00 0.00 45.98 3.18
3059 5496 3.849574 TGATCTTTAGGTTGGGTCCATCA 59.150 43.478 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.