Multiple sequence alignment - TraesCS2B01G409300

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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 TraesCS2B01G409300 chr2B 100.000 6844 0 0 1 6844 582801934 582808777 0.000000e+00 12639.0
1 TraesCS2B01G409300 chr2B 84.966 592 70 10 3548 4125 389409709 389410295 3.560000e-162 582.0
2 TraesCS2B01G409300 chr2B 86.260 524 54 11 3198 3711 582804657 582805172 2.790000e-153 553.0
3 TraesCS2B01G409300 chr2B 86.260 524 54 11 2724 3239 582805131 582805644 2.790000e-153 553.0
4 TraesCS2B01G409300 chr2B 83.029 383 39 12 2610 2986 582803867 582804229 2.380000e-84 324.0
5 TraesCS2B01G409300 chr2B 83.029 383 39 12 1934 2296 582804543 582804919 2.380000e-84 324.0
6 TraesCS2B01G409300 chr2B 80.255 471 54 7 3269 3727 582804029 582804472 1.110000e-82 318.0
7 TraesCS2B01G409300 chr2B 80.255 471 54 7 2096 2539 582805202 582805660 1.110000e-82 318.0
8 TraesCS2B01G409300 chr2A 94.118 3842 160 23 2304 6106 638687947 638684133 0.000000e+00 5782.0
9 TraesCS2B01G409300 chr2A 85.995 2135 123 73 1 2059 638689869 638687835 0.000000e+00 2124.0
10 TraesCS2B01G409300 chr2A 93.514 740 35 4 6105 6844 638683690 638682964 0.000000e+00 1088.0
11 TraesCS2B01G409300 chr2A 89.062 512 46 3 2724 3227 638687037 638686528 1.620000e-175 627.0
12 TraesCS2B01G409300 chr2A 87.218 532 46 11 3198 3717 638687510 638686989 2.750000e-163 586.0
13 TraesCS2B01G409300 chr2A 82.261 637 58 26 1934 2523 638687624 638686996 3.690000e-137 499.0
14 TraesCS2B01G409300 chr2A 94.253 261 14 1 5846 6106 638684057 638683798 1.380000e-106 398.0
15 TraesCS2B01G409300 chr2A 81.529 471 56 14 2099 2542 638686963 638686497 6.530000e-95 359.0
16 TraesCS2B01G409300 chr2A 83.475 236 33 3 3501 3730 638687938 638687703 1.500000e-51 215.0
17 TraesCS2B01G409300 chr2A 92.857 112 8 0 2614 2725 638687955 638687844 5.490000e-36 163.0
18 TraesCS2B01G409300 chr2D 97.181 2199 45 7 3708 5893 495097839 495100033 0.000000e+00 3701.0
19 TraesCS2B01G409300 chr2D 93.067 1630 79 11 2103 3705 495096131 495097753 0.000000e+00 2353.0
20 TraesCS2B01G409300 chr2D 91.055 1554 64 27 534 2052 495094535 495096048 0.000000e+00 2030.0
21 TraesCS2B01G409300 chr2D 95.468 993 39 4 5855 6844 495100064 495101053 0.000000e+00 1580.0
22 TraesCS2B01G409300 chr2D 88.694 513 47 5 2724 3227 495097237 495097747 3.510000e-172 616.0
23 TraesCS2B01G409300 chr2D 86.629 531 41 15 16 536 495093989 495094499 1.670000e-155 560.0
24 TraesCS2B01G409300 chr2D 85.660 523 59 7 3198 3711 495096763 495097278 2.810000e-148 536.0
25 TraesCS2B01G409300 chr2D 89.474 247 18 3 2312 2550 495097067 495097313 8.620000e-79 305.0
26 TraesCS2B01G409300 chr2D 81.984 383 43 11 1934 2296 495096649 495097025 1.120000e-77 302.0
27 TraesCS2B01G409300 chr2D 79.355 465 55 11 3276 3727 495096131 495096567 8.680000e-74 289.0
28 TraesCS2B01G409300 chr2D 90.000 220 22 0 2298 2517 495097534 495097753 1.120000e-72 285.0
29 TraesCS2B01G409300 chr2D 78.535 396 53 22 2617 2986 495095937 495096326 1.480000e-56 231.0
30 TraesCS2B01G409300 chr2D 88.889 171 18 1 5899 6068 129947317 129947147 6.960000e-50 209.0
31 TraesCS2B01G409300 chr2D 93.069 101 7 0 6698 6798 129946762 129946662 1.540000e-31 148.0
32 TraesCS2B01G409300 chr2D 95.946 74 3 0 1979 2052 495096063 495096136 3.350000e-23 121.0
33 TraesCS2B01G409300 chr2D 100.000 36 0 0 5861 5896 495100035 495100070 4.430000e-07 67.6
34 TraesCS2B01G409300 chr1A 89.412 170 17 1 5899 6068 497217824 497217656 5.380000e-51 213.0
35 TraesCS2B01G409300 chr5D 89.937 159 15 1 5899 6056 361591043 361590885 3.240000e-48 204.0
36 TraesCS2B01G409300 chr5D 92.308 104 8 0 6700 6803 361590486 361590383 1.540000e-31 148.0
37 TraesCS2B01G409300 chr5D 85.455 110 16 0 1141 1250 494219428 494219319 1.560000e-21 115.0
38 TraesCS2B01G409300 chr5A 85.455 110 16 0 1141 1250 617210538 617210429 1.560000e-21 115.0


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 TraesCS2B01G409300 chr2B 582801934 582808777 6843 False 12639.000000 12639 100.000000 1 6844 1 chr2B.!!$F2 6843
1 TraesCS2B01G409300 chr2B 389409709 389410295 586 False 582.000000 582 84.966000 3548 4125 1 chr2B.!!$F1 577
2 TraesCS2B01G409300 chr2B 582803867 582805660 1793 False 398.333333 553 83.181333 1934 3727 6 chr2B.!!$F3 1793
3 TraesCS2B01G409300 chr2A 638682964 638689869 6905 True 1184.100000 5782 88.428200 1 6844 10 chr2A.!!$R1 6843
4 TraesCS2B01G409300 chr2D 495093989 495101053 7064 False 926.900000 3701 89.503429 16 6844 14 chr2D.!!$F1 6828

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
379 417 0.108019 ACGGGAGGAAGGAAACACAC 59.892 55.000 0.00 0.00 0.00 3.82 F
1075 1181 0.107831 CGGTTGAGGAGGTTGTTGGA 59.892 55.000 0.00 0.00 0.00 3.53 F
1098 1204 0.251209 GGCCGGGGAAGAAAAGAAGT 60.251 55.000 2.18 0.00 0.00 3.01 F
1644 1769 1.079612 GCTGGATTGCTTGCCAACC 60.080 57.895 0.00 0.00 35.99 3.77 F
1723 1853 3.623703 TCAAAGATGTGGATCCATGGTG 58.376 45.455 19.62 10.59 0.00 4.17 F
3873 4210 3.753815 TGCTCAACTGATGACATGGAAA 58.246 40.909 0.00 0.00 33.47 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 1835 0.323633 CCAAGCACCATGGATCCACA 60.324 55.000 21.47 0.0 40.56 4.17 R
1915 2045 4.095185 CCAGGTTGTTTCGACAGTTTAACA 59.905 41.667 0.00 0.0 0.00 2.41 R
3727 4051 6.843069 AAAATAAAGAACAACACATGGTGC 57.157 33.333 0.00 0.0 36.98 5.01 R
4076 4414 2.672961 TAGGAAGGCAGTGAACGATG 57.327 50.000 0.00 0.0 0.00 3.84 R
4283 4621 5.418676 CCTAACAAATAGGCCCAAATTGTG 58.581 41.667 12.77 8.3 44.72 3.33 R
6198 7019 0.177141 ATACCACCATCCGTCCAACG 59.823 55.000 0.00 0.0 42.11 4.10 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
66 67 2.124695 GTCCATTCCACGGCCTCC 60.125 66.667 0.00 0.00 0.00 4.30
80 81 4.129737 CTCCGTCCACATCCGCGT 62.130 66.667 4.92 0.00 0.00 6.01
133 134 1.604378 CTCCTCCGAACTGGGCATT 59.396 57.895 0.00 0.00 38.76 3.56
222 223 1.867233 CACCGTCCTTTTCACTGTCAG 59.133 52.381 0.00 0.00 0.00 3.51
223 224 1.202651 ACCGTCCTTTTCACTGTCAGG 60.203 52.381 4.53 0.00 0.00 3.86
260 262 3.001406 GCCACCCCACCGTACTCT 61.001 66.667 0.00 0.00 0.00 3.24
264 266 1.839747 ACCCCACCGTACTCTTGCA 60.840 57.895 0.00 0.00 0.00 4.08
265 267 1.079127 CCCCACCGTACTCTTGCAG 60.079 63.158 0.00 0.00 0.00 4.41
269 271 0.602638 CACCGTACTCTTGCAGGCAA 60.603 55.000 6.53 6.53 0.00 4.52
270 272 0.602905 ACCGTACTCTTGCAGGCAAC 60.603 55.000 1.93 0.00 0.00 4.17
272 274 1.497722 GTACTCTTGCAGGCAACGC 59.502 57.895 1.93 0.00 46.39 4.84
273 275 1.070615 TACTCTTGCAGGCAACGCA 59.929 52.632 1.93 0.00 42.69 5.24
274 276 0.950555 TACTCTTGCAGGCAACGCAG 60.951 55.000 1.93 2.45 44.44 5.18
275 277 3.606065 CTCTTGCAGGCAACGCAGC 62.606 63.158 1.93 0.00 44.44 5.25
296 298 2.228059 CAGGGATCACATGGCATTCTC 58.772 52.381 0.00 0.00 0.00 2.87
297 299 1.144503 AGGGATCACATGGCATTCTCC 59.855 52.381 0.00 1.54 0.00 3.71
298 300 1.233019 GGATCACATGGCATTCTCCG 58.767 55.000 0.00 0.00 0.00 4.63
299 301 1.233019 GATCACATGGCATTCTCCGG 58.767 55.000 0.00 0.00 0.00 5.14
300 302 0.179009 ATCACATGGCATTCTCCGGG 60.179 55.000 0.00 0.00 0.00 5.73
301 303 1.825191 CACATGGCATTCTCCGGGG 60.825 63.158 0.00 0.00 0.00 5.73
302 304 2.308722 ACATGGCATTCTCCGGGGT 61.309 57.895 0.00 0.00 0.00 4.95
303 305 1.825191 CATGGCATTCTCCGGGGTG 60.825 63.158 0.00 0.00 0.00 4.61
304 306 3.060614 ATGGCATTCTCCGGGGTGG 62.061 63.158 0.00 0.00 40.09 4.61
305 307 4.506255 GGCATTCTCCGGGGTGGG 62.506 72.222 0.00 0.00 38.76 4.61
321 343 2.735772 GGGGAGCGCAGAGAATCCA 61.736 63.158 11.47 0.00 33.66 3.41
370 408 4.584327 AACAAAAATCAACGGGAGGAAG 57.416 40.909 0.00 0.00 0.00 3.46
371 409 2.890945 ACAAAAATCAACGGGAGGAAGG 59.109 45.455 0.00 0.00 0.00 3.46
372 410 3.153919 CAAAAATCAACGGGAGGAAGGA 58.846 45.455 0.00 0.00 0.00 3.36
373 411 3.518992 AAAATCAACGGGAGGAAGGAA 57.481 42.857 0.00 0.00 0.00 3.36
376 414 1.133363 TCAACGGGAGGAAGGAAACA 58.867 50.000 0.00 0.00 0.00 2.83
379 417 0.108019 ACGGGAGGAAGGAAACACAC 59.892 55.000 0.00 0.00 0.00 3.82
383 421 1.474498 GGAGGAAGGAAACACACACGT 60.474 52.381 0.00 0.00 0.00 4.49
399 437 2.350498 ACACGTTTCCGACTTTCAGTTG 59.650 45.455 0.00 0.00 37.88 3.16
400 438 2.605818 CACGTTTCCGACTTTCAGTTGA 59.394 45.455 0.00 0.00 37.88 3.18
404 442 0.756294 TCCGACTTTCAGTTGAGGCA 59.244 50.000 0.00 0.00 31.05 4.75
474 516 1.227383 GAAAGGTCGGGCATGGGAT 59.773 57.895 0.00 0.00 0.00 3.85
491 533 1.379443 ATGCACATGCCCTGACTGG 60.379 57.895 0.49 0.00 41.18 4.00
545 625 1.152989 CGGTTGGACCAACGAACGAA 61.153 55.000 27.08 0.00 44.36 3.85
653 742 1.286880 CTCCAAAACTGCCAAGGCG 59.713 57.895 6.60 4.13 45.51 5.52
680 769 6.352016 TGCAGGATCCATCTAACTAATCTC 57.648 41.667 15.82 0.00 0.00 2.75
681 770 5.047731 TGCAGGATCCATCTAACTAATCTCG 60.048 44.000 15.82 0.00 0.00 4.04
685 774 5.392165 GGATCCATCTAACTAATCTCGTCGG 60.392 48.000 6.95 0.00 0.00 4.79
700 789 1.423395 GTCGGCTCAACTCAACTCAG 58.577 55.000 0.00 0.00 0.00 3.35
702 791 1.686587 TCGGCTCAACTCAACTCAGAA 59.313 47.619 0.00 0.00 0.00 3.02
704 793 2.872245 CGGCTCAACTCAACTCAGAAAA 59.128 45.455 0.00 0.00 0.00 2.29
705 794 3.059325 CGGCTCAACTCAACTCAGAAAAG 60.059 47.826 0.00 0.00 0.00 2.27
706 795 4.130118 GGCTCAACTCAACTCAGAAAAGA 58.870 43.478 0.00 0.00 0.00 2.52
707 796 4.576463 GGCTCAACTCAACTCAGAAAAGAA 59.424 41.667 0.00 0.00 0.00 2.52
708 797 5.066505 GGCTCAACTCAACTCAGAAAAGAAA 59.933 40.000 0.00 0.00 0.00 2.52
709 798 6.404734 GGCTCAACTCAACTCAGAAAAGAAAA 60.405 38.462 0.00 0.00 0.00 2.29
710 799 7.029563 GCTCAACTCAACTCAGAAAAGAAAAA 58.970 34.615 0.00 0.00 0.00 1.94
711 800 7.219726 GCTCAACTCAACTCAGAAAAGAAAAAG 59.780 37.037 0.00 0.00 0.00 2.27
742 831 1.595993 CGTCGTCTGGTCCCAGTCAT 61.596 60.000 12.88 0.00 43.96 3.06
772 861 2.499205 GGCGTGATCCGTCCATCA 59.501 61.111 5.66 0.00 39.32 3.07
773 862 1.592669 GGCGTGATCCGTCCATCAG 60.593 63.158 5.66 0.00 39.32 2.90
774 863 1.437573 GCGTGATCCGTCCATCAGA 59.562 57.895 5.66 0.00 39.32 3.27
813 908 1.449601 ACGTTAATGGCCTGCTCGG 60.450 57.895 3.32 0.00 0.00 4.63
827 922 1.416049 CTCGGTCGTTGTTCATGCG 59.584 57.895 0.00 0.00 0.00 4.73
828 923 2.202171 CGGTCGTTGTTCATGCGC 60.202 61.111 0.00 0.00 0.00 6.09
829 924 2.202171 GGTCGTTGTTCATGCGCG 60.202 61.111 0.00 0.00 0.00 6.86
830 925 2.865151 GTCGTTGTTCATGCGCGC 60.865 61.111 27.26 27.26 0.00 6.86
831 926 4.083600 TCGTTGTTCATGCGCGCC 62.084 61.111 30.77 13.48 0.00 6.53
833 928 4.776647 GTTGTTCATGCGCGCCCC 62.777 66.667 30.77 11.99 0.00 5.80
858 953 5.321625 TCCCTCACTCCCTCCCTATTAATAT 59.678 44.000 0.00 0.00 0.00 1.28
860 955 5.663556 CCTCACTCCCTCCCTATTAATATCC 59.336 48.000 0.00 0.00 0.00 2.59
907 1003 3.802418 AAACAACCGGAGCTCGCGT 62.802 57.895 9.46 10.37 37.59 6.01
997 1103 4.530857 CCCCACCACGATCTCGCC 62.531 72.222 0.00 0.00 44.43 5.54
1027 1133 4.675029 CGTGTTTCCGTCGCCCCT 62.675 66.667 0.00 0.00 0.00 4.79
1075 1181 0.107831 CGGTTGAGGAGGTTGTTGGA 59.892 55.000 0.00 0.00 0.00 3.53
1098 1204 0.251209 GGCCGGGGAAGAAAAGAAGT 60.251 55.000 2.18 0.00 0.00 3.01
1099 1205 1.617322 GCCGGGGAAGAAAAGAAGTT 58.383 50.000 2.18 0.00 0.00 2.66
1100 1206 2.553685 GGCCGGGGAAGAAAAGAAGTTA 60.554 50.000 2.18 0.00 0.00 2.24
1101 1207 2.747989 GCCGGGGAAGAAAAGAAGTTAG 59.252 50.000 2.18 0.00 0.00 2.34
1257 1374 2.683933 AGATCAAGGTCCCGCCGT 60.684 61.111 0.00 0.00 43.70 5.68
1258 1375 2.202892 GATCAAGGTCCCGCCGTC 60.203 66.667 0.00 0.00 43.70 4.79
1278 1395 5.178797 CGTCTTCTCTTCTCTCTTCTCTCT 58.821 45.833 0.00 0.00 0.00 3.10
1280 1397 6.183360 CGTCTTCTCTTCTCTCTTCTCTCTTC 60.183 46.154 0.00 0.00 0.00 2.87
1281 1398 6.094186 GTCTTCTCTTCTCTCTTCTCTCTTCC 59.906 46.154 0.00 0.00 0.00 3.46
1320 1437 2.686405 GACCGGACCTTGACTTTGTTTT 59.314 45.455 9.46 0.00 0.00 2.43
1321 1438 2.425668 ACCGGACCTTGACTTTGTTTTG 59.574 45.455 9.46 0.00 0.00 2.44
1322 1439 2.459934 CGGACCTTGACTTTGTTTTGC 58.540 47.619 0.00 0.00 0.00 3.68
1324 1441 3.428862 CGGACCTTGACTTTGTTTTGCTT 60.429 43.478 0.00 0.00 0.00 3.91
1325 1442 4.201970 CGGACCTTGACTTTGTTTTGCTTA 60.202 41.667 0.00 0.00 0.00 3.09
1327 1444 5.920840 GGACCTTGACTTTGTTTTGCTTATC 59.079 40.000 0.00 0.00 0.00 1.75
1328 1445 6.460953 GGACCTTGACTTTGTTTTGCTTATCA 60.461 38.462 0.00 0.00 0.00 2.15
1329 1446 7.054491 ACCTTGACTTTGTTTTGCTTATCAT 57.946 32.000 0.00 0.00 0.00 2.45
1330 1447 7.147976 ACCTTGACTTTGTTTTGCTTATCATC 58.852 34.615 0.00 0.00 0.00 2.92
1537 1662 5.183713 TGTCAATTTGATTGCGATTTCTCCT 59.816 36.000 1.78 0.00 40.05 3.69
1598 1723 3.695830 AGCGATTGTGACCCTAAAAGA 57.304 42.857 0.00 0.00 0.00 2.52
1644 1769 1.079612 GCTGGATTGCTTGCCAACC 60.080 57.895 0.00 0.00 35.99 3.77
1723 1853 3.623703 TCAAAGATGTGGATCCATGGTG 58.376 45.455 19.62 10.59 0.00 4.17
1804 1934 5.467063 GCCTGTATGCTTAGTTTAGGACATC 59.533 44.000 0.00 0.00 0.00 3.06
1827 1957 5.129980 TCATGTAGATTCTCCTTGCTGTCAT 59.870 40.000 0.00 0.00 0.00 3.06
1881 2011 5.981088 TCCTTTTTAATGAGAGCATGCAA 57.019 34.783 21.98 0.00 34.26 4.08
1882 2012 6.534475 TCCTTTTTAATGAGAGCATGCAAT 57.466 33.333 21.98 7.52 34.26 3.56
1907 2037 6.098266 TGCTCCTCTGTTATTACAAGCTCATA 59.902 38.462 7.53 0.00 36.07 2.15
3727 4051 8.452989 AAGCGCTATTTTCTTAGAAATTGTTG 57.547 30.769 12.05 1.14 31.96 3.33
3748 4075 5.528043 TGCACCATGTGTTGTTCTTTATT 57.472 34.783 0.00 0.00 35.75 1.40
3846 4183 5.940470 ACAGGTTGATCCAGATGAAGTAAAC 59.060 40.000 0.00 0.00 39.02 2.01
3873 4210 3.753815 TGCTCAACTGATGACATGGAAA 58.246 40.909 0.00 0.00 33.47 3.13
4076 4414 6.030228 GCTATGCAATTTCAGTGTCTTTACC 58.970 40.000 0.00 0.00 0.00 2.85
4268 4606 7.696755 TGCTGCATATAAACTCTTTACACATG 58.303 34.615 0.00 0.00 0.00 3.21
4407 4745 4.672587 TGGGAAGTCTATTTCTGGATCG 57.327 45.455 0.00 0.00 0.00 3.69
4428 4766 3.125316 CGACCTTTGTTATTCAGGTGAGC 59.875 47.826 0.00 0.00 32.35 4.26
4439 4777 4.623932 TTCAGGTGAGCTGTGATAAACT 57.376 40.909 11.78 0.00 0.00 2.66
4445 4783 4.153117 GGTGAGCTGTGATAAACTGTTGAG 59.847 45.833 0.00 0.00 0.00 3.02
4459 4797 6.867662 AACTGTTGAGTTCTTGAATGGTAG 57.132 37.500 0.00 0.00 38.01 3.18
4488 4826 1.904287 AGCGAGTGCCATGGTAAAAA 58.096 45.000 14.67 0.00 44.31 1.94
4852 5190 4.552166 TTGCTATTATCCTTTTGCGCTC 57.448 40.909 9.73 0.00 0.00 5.03
4883 5221 7.283127 TGTGGCCTAAATCATTTTCACTAGATC 59.717 37.037 3.32 0.00 0.00 2.75
5209 5548 1.363744 CAACCGATCCAGAAGCTGAC 58.636 55.000 0.00 0.00 32.44 3.51
5461 5801 1.826720 GCCTTTGCCATCTCATTCCAA 59.173 47.619 0.00 0.00 0.00 3.53
5500 5840 1.818674 CCGGCAGTTTCCTTATGCTTT 59.181 47.619 0.00 0.00 39.88 3.51
5844 6184 8.925161 ATTGAAATAATTTTCGGTGTACATGG 57.075 30.769 0.00 0.00 43.49 3.66
5962 6674 7.973944 AGAGTTGTTGAATGTTTACCAAAAGTC 59.026 33.333 0.00 0.00 0.00 3.01
6073 6785 8.887717 AGATTACTTCTGCAAGATTCATGTAAC 58.112 33.333 0.00 0.00 46.36 2.50
6085 6797 8.777413 CAAGATTCATGTAACTGAGAGTTTCAA 58.223 33.333 0.00 0.00 38.62 2.69
6135 6956 4.874970 ACCAGAACAATTGCATCTGTTTC 58.125 39.130 27.15 14.47 39.10 2.78
6149 6970 5.345202 GCATCTGTTTCTCTTTTTGCATGAG 59.655 40.000 0.00 0.00 0.00 2.90
6181 7002 7.983307 AGATTCATACAAATTCAGTCTCAAGC 58.017 34.615 0.00 0.00 0.00 4.01
6191 7012 0.035458 AGTCTCAAGCCAAACCCTCG 59.965 55.000 0.00 0.00 0.00 4.63
6310 7131 4.158394 ACTGCTGAAGTTCAACAACAACAT 59.842 37.500 10.06 0.00 34.57 2.71
6311 7132 5.356751 ACTGCTGAAGTTCAACAACAACATA 59.643 36.000 10.06 0.00 34.57 2.29
6314 7135 6.751425 TGCTGAAGTTCAACAACAACATAAAG 59.249 34.615 6.49 0.00 34.60 1.85
6357 7178 6.985188 TGATGGATAGAACACAAAAGCTAC 57.015 37.500 0.00 0.00 0.00 3.58
6384 7205 2.553602 TGTGCACTGCATTTAGGAACTG 59.446 45.455 19.41 0.00 41.91 3.16
6491 7312 1.073025 AGGCAATGCGAGGACACAA 59.927 52.632 0.00 0.00 0.00 3.33
6501 7322 2.413837 CGAGGACACAAAACTTCGGAT 58.586 47.619 0.00 0.00 33.29 4.18
6515 7336 4.690122 ACTTCGGATTATTTGGTACCTCG 58.310 43.478 14.36 4.63 0.00 4.63
6536 7357 6.128172 CCTCGTCATAAAAGTTCAGCAGAAAT 60.128 38.462 0.00 0.00 35.08 2.17
6575 7396 1.503542 CGGCTTGACCAATGCTGAC 59.496 57.895 7.00 0.00 39.03 3.51
6602 7423 4.202151 GCCTCATTGGGTGTAATTTCATCC 60.202 45.833 7.40 7.40 38.93 3.51
6706 7527 2.229543 TGTCTGCAATTGATGTTGAGGC 59.770 45.455 10.34 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 4.147322 GCAACGCGGATGTGGACG 62.147 66.667 12.47 0.00 0.00 4.79
110 111 1.743252 CCAGTTCGGAGGAGCAAGC 60.743 63.158 0.00 0.00 36.56 4.01
269 271 2.673200 ATGTGATCCCTGGCTGCGT 61.673 57.895 0.00 0.00 0.00 5.24
270 272 2.184830 CATGTGATCCCTGGCTGCG 61.185 63.158 0.00 0.00 0.00 5.18
272 274 4.573210 CCATGTGATCCCTGGCTG 57.427 61.111 0.00 0.00 0.00 4.85
275 277 1.133575 AGAATGCCATGTGATCCCTGG 60.134 52.381 0.00 0.00 0.00 4.45
276 278 2.228059 GAGAATGCCATGTGATCCCTG 58.772 52.381 0.00 0.00 0.00 4.45
277 279 1.144503 GGAGAATGCCATGTGATCCCT 59.855 52.381 0.00 0.00 0.00 4.20
278 280 1.613836 GGAGAATGCCATGTGATCCC 58.386 55.000 0.00 0.00 0.00 3.85
279 281 1.233019 CGGAGAATGCCATGTGATCC 58.767 55.000 0.00 0.00 0.00 3.36
280 282 1.233019 CCGGAGAATGCCATGTGATC 58.767 55.000 0.00 0.00 0.00 2.92
281 283 0.179009 CCCGGAGAATGCCATGTGAT 60.179 55.000 0.73 0.00 0.00 3.06
282 284 1.224315 CCCGGAGAATGCCATGTGA 59.776 57.895 0.73 0.00 0.00 3.58
300 302 2.932130 GATTCTCTGCGCTCCCCACC 62.932 65.000 9.73 0.00 0.00 4.61
301 303 1.522580 GATTCTCTGCGCTCCCCAC 60.523 63.158 9.73 0.00 0.00 4.61
302 304 2.735772 GGATTCTCTGCGCTCCCCA 61.736 63.158 9.73 0.00 0.00 4.96
303 305 2.110006 GGATTCTCTGCGCTCCCC 59.890 66.667 9.73 0.00 0.00 4.81
304 306 1.227497 CTGGATTCTCTGCGCTCCC 60.227 63.158 9.73 0.00 0.00 4.30
305 307 1.886777 GCTGGATTCTCTGCGCTCC 60.887 63.158 9.73 6.56 0.00 4.70
399 437 0.755698 TAGGTCCGTCCATCTGCCTC 60.756 60.000 0.00 0.00 39.02 4.70
400 438 1.043673 GTAGGTCCGTCCATCTGCCT 61.044 60.000 0.00 0.00 39.02 4.75
404 442 2.478890 CGCGTAGGTCCGTCCATCT 61.479 63.158 0.00 0.00 39.02 2.90
469 511 2.043752 CAGGGCATGTGCATCCCA 60.044 61.111 15.58 0.00 42.52 4.37
474 516 2.034532 CCAGTCAGGGCATGTGCA 59.965 61.111 7.36 0.00 44.36 4.57
491 533 0.749454 CTACTTGATGGCCCACCTGC 60.749 60.000 0.00 0.00 36.63 4.85
503 545 1.271379 CGGTGTGCTGGTACTACTTGA 59.729 52.381 0.00 0.00 0.00 3.02
530 572 0.595567 CTCGTTCGTTCGTTGGTCCA 60.596 55.000 0.00 0.00 0.00 4.02
535 615 1.407329 CTCGCTCGTTCGTTCGTTG 59.593 57.895 2.67 0.06 0.00 4.10
538 618 2.056087 GATGCTCGCTCGTTCGTTCG 62.056 60.000 0.00 0.00 0.00 3.95
577 657 2.944390 AGGAAAATCGGGGCCCCA 60.944 61.111 40.06 26.84 35.37 4.96
590 679 0.528017 CAGCTGTGTAGAGCGAGGAA 59.472 55.000 5.25 0.00 44.24 3.36
623 712 4.724036 GCAGTTTTGGAGCGTAATTACTCG 60.724 45.833 13.56 2.77 33.55 4.18
653 742 2.158842 AGTTAGATGGATCCTGCAGCAC 60.159 50.000 14.23 1.15 0.00 4.40
680 769 0.318699 TGAGTTGAGTTGAGCCGACG 60.319 55.000 0.00 0.00 0.00 5.12
681 770 1.000163 TCTGAGTTGAGTTGAGCCGAC 60.000 52.381 0.00 0.00 0.00 4.79
685 774 5.741388 TTCTTTTCTGAGTTGAGTTGAGC 57.259 39.130 0.00 0.00 0.00 4.26
772 861 2.352032 CGGCCCTCTTCTTCCGTCT 61.352 63.158 0.00 0.00 37.33 4.18
773 862 2.184579 CGGCCCTCTTCTTCCGTC 59.815 66.667 0.00 0.00 37.33 4.79
774 863 3.391382 CCGGCCCTCTTCTTCCGT 61.391 66.667 0.00 0.00 40.23 4.69
776 865 2.269241 CACCGGCCCTCTTCTTCC 59.731 66.667 0.00 0.00 0.00 3.46
813 908 2.865151 GCGCGCATGAACAACGAC 60.865 61.111 29.10 0.00 0.00 4.34
829 924 4.423209 AGGGAGTGAGGGAGGGGC 62.423 72.222 0.00 0.00 0.00 5.80
830 925 2.041405 GAGGGAGTGAGGGAGGGG 60.041 72.222 0.00 0.00 0.00 4.79
831 926 2.041405 GGAGGGAGTGAGGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
832 927 1.297409 TAGGGAGGGAGTGAGGGAGG 61.297 65.000 0.00 0.00 0.00 4.30
833 928 0.863956 ATAGGGAGGGAGTGAGGGAG 59.136 60.000 0.00 0.00 0.00 4.30
834 929 1.330155 AATAGGGAGGGAGTGAGGGA 58.670 55.000 0.00 0.00 0.00 4.20
835 930 3.346146 TTAATAGGGAGGGAGTGAGGG 57.654 52.381 0.00 0.00 0.00 4.30
836 931 5.663556 GGATATTAATAGGGAGGGAGTGAGG 59.336 48.000 1.02 0.00 0.00 3.86
837 932 6.507568 AGGATATTAATAGGGAGGGAGTGAG 58.492 44.000 1.02 0.00 0.00 3.51
838 933 6.500490 AGGATATTAATAGGGAGGGAGTGA 57.500 41.667 1.02 0.00 0.00 3.41
839 934 5.663556 GGAGGATATTAATAGGGAGGGAGTG 59.336 48.000 1.02 0.00 0.00 3.51
840 935 5.566039 AGGAGGATATTAATAGGGAGGGAGT 59.434 44.000 1.02 0.00 0.00 3.85
845 940 6.067901 AGGAGGAGGAGGATATTAATAGGGAG 60.068 46.154 1.02 0.00 0.00 4.30
858 953 2.041265 GCCCAAGGAGGAGGAGGA 59.959 66.667 0.00 0.00 41.22 3.71
860 955 1.617839 AAGGCCCAAGGAGGAGGAG 60.618 63.158 0.00 0.00 41.22 3.69
907 1003 3.101187 TCCGGAGATCGAGGGGGA 61.101 66.667 0.00 0.00 42.43 4.81
984 1090 4.779733 AGGGGGCGAGATCGTGGT 62.780 66.667 3.94 0.00 42.22 4.16
1023 1129 0.321653 CGAAAGGGACAGACAAGGGG 60.322 60.000 0.00 0.00 0.00 4.79
1027 1133 1.072505 GGGCGAAAGGGACAGACAA 59.927 57.895 0.00 0.00 0.00 3.18
1257 1374 6.180472 GGAAGAGAGAAGAGAGAAGAGAAGA 58.820 44.000 0.00 0.00 0.00 2.87
1258 1375 5.358160 GGGAAGAGAGAAGAGAGAAGAGAAG 59.642 48.000 0.00 0.00 0.00 2.85
1278 1395 2.042843 GGCGAGGAGAGGAGGGAA 60.043 66.667 0.00 0.00 0.00 3.97
1306 1423 7.373493 AGATGATAAGCAAAACAAAGTCAAGG 58.627 34.615 0.00 0.00 0.00 3.61
1320 1437 4.591321 AAGGAACCCAAGATGATAAGCA 57.409 40.909 0.00 0.00 0.00 3.91
1321 1438 4.339530 GGAAAGGAACCCAAGATGATAAGC 59.660 45.833 0.00 0.00 0.00 3.09
1322 1439 5.760131 AGGAAAGGAACCCAAGATGATAAG 58.240 41.667 0.00 0.00 0.00 1.73
1324 1441 5.629133 CGAAGGAAAGGAACCCAAGATGATA 60.629 44.000 0.00 0.00 0.00 2.15
1325 1442 4.604156 GAAGGAAAGGAACCCAAGATGAT 58.396 43.478 0.00 0.00 0.00 2.45
1327 1444 2.749621 CGAAGGAAAGGAACCCAAGATG 59.250 50.000 0.00 0.00 0.00 2.90
1328 1445 2.880167 GCGAAGGAAAGGAACCCAAGAT 60.880 50.000 0.00 0.00 0.00 2.40
1329 1446 1.544759 GCGAAGGAAAGGAACCCAAGA 60.545 52.381 0.00 0.00 0.00 3.02
1330 1447 0.881796 GCGAAGGAAAGGAACCCAAG 59.118 55.000 0.00 0.00 0.00 3.61
1537 1662 2.946329 TGCGTCTTGTTTTAGGCTTTCA 59.054 40.909 0.00 0.00 0.00 2.69
1598 1723 7.470289 TTTTGCGTGTGTTAATTTGCTTATT 57.530 28.000 0.00 0.00 0.00 1.40
1644 1769 4.116961 CAATGGATGTAAAAGCATGCCAG 58.883 43.478 15.66 0.00 36.54 4.85
1707 1833 1.679680 CAAGCACCATGGATCCACATC 59.320 52.381 21.47 4.92 0.00 3.06
1709 1835 0.323633 CCAAGCACCATGGATCCACA 60.324 55.000 21.47 0.00 40.56 4.17
1723 1853 6.873605 ACAAAAATAACCTAAGAATGCCAAGC 59.126 34.615 0.00 0.00 0.00 4.01
1804 1934 4.763073 TGACAGCAAGGAGAATCTACATG 58.237 43.478 0.00 0.00 33.73 3.21
1881 2011 5.104776 TGAGCTTGTAATAACAGAGGAGCAT 60.105 40.000 0.00 0.00 37.93 3.79
1882 2012 4.222810 TGAGCTTGTAATAACAGAGGAGCA 59.777 41.667 0.00 0.00 37.93 4.26
1907 2037 7.531716 TGTTTCGACAGTTTAACAACAGAAAT 58.468 30.769 0.00 0.00 35.05 2.17
1915 2045 4.095185 CCAGGTTGTTTCGACAGTTTAACA 59.905 41.667 0.00 0.00 0.00 2.41
3727 4051 6.843069 AAAATAAAGAACAACACATGGTGC 57.157 33.333 0.00 0.00 36.98 5.01
3748 4075 4.832266 TGCCTTGGCTTTTCAGAATCTAAA 59.168 37.500 13.18 0.00 0.00 1.85
3757 4084 2.884639 GACTTACTGCCTTGGCTTTTCA 59.115 45.455 13.18 0.00 0.00 2.69
3999 4337 4.262463 GCTGGAATATCGGTATGAGTTCCA 60.262 45.833 7.97 7.97 45.59 3.53
4076 4414 2.672961 TAGGAAGGCAGTGAACGATG 57.327 50.000 0.00 0.00 0.00 3.84
4268 4606 9.846248 GCCCAAATTGTGATCATATTAGTAATC 57.154 33.333 0.00 0.00 0.00 1.75
4283 4621 5.418676 CCTAACAAATAGGCCCAAATTGTG 58.581 41.667 12.77 8.30 44.72 3.33
4407 4745 4.154918 CAGCTCACCTGAATAACAAAGGTC 59.845 45.833 0.00 0.00 42.51 3.85
4428 4766 7.482654 TCAAGAACTCAACAGTTTATCACAG 57.517 36.000 0.00 0.00 43.37 3.66
4439 4777 7.279615 TCTTTCTACCATTCAAGAACTCAACA 58.720 34.615 0.00 0.00 31.62 3.33
4445 4783 9.036671 GCTACTATCTTTCTACCATTCAAGAAC 57.963 37.037 0.00 0.00 31.62 3.01
4459 4797 3.438297 TGGCACTCGCTACTATCTTTC 57.562 47.619 0.00 0.00 38.60 2.62
4488 4826 9.965824 CTATGTTTGAACAGACTTATTTTGGTT 57.034 29.630 2.77 0.00 43.04 3.67
4845 5183 2.334946 GGCCACATCAAGAGCGCAA 61.335 57.895 11.47 0.00 0.00 4.85
4852 5190 6.532657 GTGAAAATGATTTAGGCCACATCAAG 59.467 38.462 5.01 0.00 30.79 3.02
4971 5309 8.959734 ATTATCACAATATTCGCACATCAATG 57.040 30.769 0.00 0.00 0.00 2.82
5055 5393 6.830324 AGCAATCAGAAAATAGGTTGCTCATA 59.170 34.615 7.07 0.00 46.45 2.15
5209 5548 3.376546 GGTGGTACAGTACTCTTACCTCG 59.623 52.174 22.57 2.31 41.80 4.63
5285 5624 8.131100 TGAGACATTCAGAAAACAGAATTGAAC 58.869 33.333 0.00 0.00 32.43 3.18
5461 5801 4.747810 CCGGCTCAAGCAAAAAGATAATT 58.252 39.130 4.13 0.00 44.36 1.40
5500 5840 3.237746 TGAATGTTCTGCCCCATCAAAA 58.762 40.909 0.00 0.00 0.00 2.44
5509 5849 4.159135 ACATGAATCCTTGAATGTTCTGCC 59.841 41.667 0.00 0.00 28.99 4.85
5844 6184 3.350833 AGAACAAACCCATCATCTCTGC 58.649 45.455 0.00 0.00 0.00 4.26
5996 6708 6.268387 AGACCAGAAATGTTGAAACCAATGAT 59.732 34.615 0.00 0.00 0.00 2.45
6073 6785 5.239306 TGCCATAAGTTGTTGAAACTCTCAG 59.761 40.000 0.00 0.00 34.81 3.35
6085 6797 7.701539 TTGATATTTGTCTGCCATAAGTTGT 57.298 32.000 0.00 0.00 0.00 3.32
6135 6956 2.481568 TCGTCAGCTCATGCAAAAAGAG 59.518 45.455 0.00 0.00 42.74 2.85
6149 6970 6.036517 ACTGAATTTGTATGAATCTCGTCAGC 59.963 38.462 0.00 0.00 0.00 4.26
6181 7002 4.426313 GAGGCCCCGAGGGTTTGG 62.426 72.222 7.48 0.00 46.51 3.28
6198 7019 0.177141 ATACCACCATCCGTCCAACG 59.823 55.000 0.00 0.00 42.11 4.10
6310 7131 9.558396 TCATCGGTAGTTTTAGGTTTTTCTTTA 57.442 29.630 0.00 0.00 0.00 1.85
6311 7132 8.454570 TCATCGGTAGTTTTAGGTTTTTCTTT 57.545 30.769 0.00 0.00 0.00 2.52
6314 7135 7.120138 TCCATCATCGGTAGTTTTAGGTTTTTC 59.880 37.037 0.00 0.00 0.00 2.29
6357 7178 1.518056 AAATGCAGTGCACAGGACGG 61.518 55.000 22.44 2.04 43.04 4.79
6384 7205 6.706270 TCACATAGTTGAAAGAACACCTCTTC 59.294 38.462 0.00 0.00 44.00 2.87
6478 7299 1.531149 CGAAGTTTTGTGTCCTCGCAT 59.469 47.619 0.00 0.00 33.92 4.73
6491 7312 5.583457 CGAGGTACCAAATAATCCGAAGTTT 59.417 40.000 15.94 0.00 0.00 2.66
6501 7322 8.851541 AACTTTTATGACGAGGTACCAAATAA 57.148 30.769 15.94 7.53 0.00 1.40
6515 7336 8.579682 AACAATTTCTGCTGAACTTTTATGAC 57.420 30.769 5.41 0.00 31.02 3.06
6536 7357 1.064946 CCGCAAACCTCGCAAACAA 59.935 52.632 0.00 0.00 0.00 2.83
6575 7396 0.251916 TTACACCCAATGAGGCTCGG 59.748 55.000 10.42 7.32 35.39 4.63
6612 7433 0.801872 CGCAAACCGACATTGATGGA 59.198 50.000 6.05 0.00 40.02 3.41
6653 7474 1.133253 CAACGTTGCATCTGCTCCG 59.867 57.895 16.51 7.91 42.66 4.63
6677 7498 2.867624 TCAATTGCAGACAAGAAGGCT 58.132 42.857 0.00 0.00 39.69 4.58
6706 7527 0.962356 AAAATCCACCTGCGGCTCTG 60.962 55.000 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.