Multiple sequence alignment - TraesCS5B01G072000

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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 TraesCS5B01G072000 chr5B 100.000 3053 0 0 1 3053 83678744 83675692 0.000000e+00 5638.0
1 TraesCS5B01G072000 chr5B 93.944 677 40 1 2331 3006 602121328 602122004 0.000000e+00 1022.0
2 TraesCS5B01G072000 chr5B 76.941 850 158 30 1136 1969 420714283 420715110 1.670000e-122 449.0
3 TraesCS5B01G072000 chr5B 76.515 396 75 9 1199 1591 419727600 419727980 1.860000e-47 200.0
4 TraesCS5B01G072000 chr5B 73.250 557 117 27 1290 1833 420922409 420921872 1.130000e-39 174.0
5 TraesCS5B01G072000 chr5D 88.791 1936 148 33 365 2256 75355198 75353288 0.000000e+00 2309.0
6 TraesCS5B01G072000 chr5D 77.765 904 161 33 1082 1968 355794498 355795378 1.250000e-143 520.0
7 TraesCS5B01G072000 chr5D 77.340 406 77 10 1184 1586 355076801 355077194 3.060000e-55 226.0
8 TraesCS5B01G072000 chr5D 78.505 321 54 13 45 356 439789471 439789785 2.400000e-46 196.0
9 TraesCS5B01G072000 chr5D 78.846 312 45 14 1286 1594 355796331 355796038 1.120000e-44 191.0
10 TraesCS5B01G072000 chr5D 73.788 557 114 27 1290 1833 356120569 356121106 1.120000e-44 191.0
11 TraesCS5B01G072000 chr5D 76.131 398 73 13 1199 1591 354941451 354941831 4.020000e-44 189.0
12 TraesCS5B01G072000 chr5A 92.909 1523 67 16 741 2238 70483378 70481872 0.000000e+00 2176.0
13 TraesCS5B01G072000 chr5A 85.588 680 86 11 23 698 70484696 70484025 0.000000e+00 702.0
14 TraesCS5B01G072000 chr5A 77.913 901 161 31 1082 1969 457516833 457515958 7.500000e-146 527.0
15 TraesCS5B01G072000 chr5A 87.013 154 8 6 2106 2255 70480007 70479862 2.440000e-36 163.0
16 TraesCS5B01G072000 chr5A 98.113 53 1 0 3001 3053 147434353 147434301 3.240000e-15 93.5
17 TraesCS5B01G072000 chr1B 93.881 670 38 3 2339 3006 56454474 56455142 0.000000e+00 1007.0
18 TraesCS5B01G072000 chr1B 77.041 392 60 24 4 374 246455744 246456126 6.680000e-47 198.0
19 TraesCS5B01G072000 chr6B 93.205 677 45 1 2331 3006 620439012 620439688 0.000000e+00 994.0
20 TraesCS5B01G072000 chr6B 92.773 678 47 2 2331 3006 176313045 176313722 0.000000e+00 979.0
21 TraesCS5B01G072000 chr4B 93.205 677 45 1 2331 3006 623051257 623050581 0.000000e+00 994.0
22 TraesCS5B01G072000 chr4B 96.491 57 1 1 2997 3053 400850003 400849948 3.240000e-15 93.5
23 TraesCS5B01G072000 chr7B 93.068 678 44 3 2331 3006 102921032 102921708 0.000000e+00 989.0
24 TraesCS5B01G072000 chr7B 93.175 674 45 1 2331 3003 661495530 661496203 0.000000e+00 989.0
25 TraesCS5B01G072000 chr7B 92.910 677 47 1 2331 3006 444835081 444834405 0.000000e+00 983.0
26 TraesCS5B01G072000 chr7B 82.156 269 38 9 47 310 453114625 453114362 3.960000e-54 222.0
27 TraesCS5B01G072000 chr7B 80.612 98 16 3 402 497 327155754 327155850 4.220000e-09 73.1
28 TraesCS5B01G072000 chr3B 93.274 669 43 2 2339 3006 493685026 493685693 0.000000e+00 985.0
29 TraesCS5B01G072000 chr6D 84.836 244 31 6 76 316 28678930 28678690 1.090000e-59 241.0
30 TraesCS5B01G072000 chr6D 89.041 73 4 3 2981 3053 171560655 171560723 1.510000e-13 87.9
31 TraesCS5B01G072000 chr4D 79.076 368 60 11 1 356 51845173 51845535 1.410000e-58 237.0
32 TraesCS5B01G072000 chr4D 81.550 271 43 7 45 310 12696214 12696482 1.840000e-52 217.0
33 TraesCS5B01G072000 chr4A 78.976 371 60 12 1 356 571741198 571740831 1.410000e-58 237.0
34 TraesCS5B01G072000 chr2A 82.824 262 36 9 48 304 777923523 777923780 3.060000e-55 226.0
35 TraesCS5B01G072000 chr2A 98.113 53 1 0 3001 3053 649302571 649302519 3.240000e-15 93.5
36 TraesCS5B01G072000 chr2A 88.889 72 7 1 2982 3053 303889136 303889206 1.510000e-13 87.9
37 TraesCS5B01G072000 chr2A 89.855 69 4 3 2986 3053 147347941 147348007 5.420000e-13 86.1
38 TraesCS5B01G072000 chr7D 74.272 412 85 17 1197 1599 125909133 125909532 1.470000e-33 154.0
39 TraesCS5B01G072000 chr1D 98.182 55 1 0 2999 3053 202257948 202257894 2.510000e-16 97.1
40 TraesCS5B01G072000 chr6A 87.013 77 5 3 2980 3053 514743857 514743783 7.020000e-12 82.4
41 TraesCS5B01G072000 chr2D 86.842 76 6 4 2980 3052 440903181 440903107 7.020000e-12 82.4


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 TraesCS5B01G072000 chr5B 83675692 83678744 3052 True 5638.000000 5638 100.000000 1 3053 1 chr5B.!!$R1 3052
1 TraesCS5B01G072000 chr5B 602121328 602122004 676 False 1022.000000 1022 93.944000 2331 3006 1 chr5B.!!$F3 675
2 TraesCS5B01G072000 chr5B 420714283 420715110 827 False 449.000000 449 76.941000 1136 1969 1 chr5B.!!$F2 833
3 TraesCS5B01G072000 chr5D 75353288 75355198 1910 True 2309.000000 2309 88.791000 365 2256 1 chr5D.!!$R1 1891
4 TraesCS5B01G072000 chr5D 355794498 355795378 880 False 520.000000 520 77.765000 1082 1968 1 chr5D.!!$F3 886
5 TraesCS5B01G072000 chr5A 70479862 70484696 4834 True 1013.666667 2176 88.503333 23 2255 3 chr5A.!!$R3 2232
6 TraesCS5B01G072000 chr5A 457515958 457516833 875 True 527.000000 527 77.913000 1082 1969 1 chr5A.!!$R2 887
7 TraesCS5B01G072000 chr1B 56454474 56455142 668 False 1007.000000 1007 93.881000 2339 3006 1 chr1B.!!$F1 667
8 TraesCS5B01G072000 chr6B 620439012 620439688 676 False 994.000000 994 93.205000 2331 3006 1 chr6B.!!$F2 675
9 TraesCS5B01G072000 chr6B 176313045 176313722 677 False 979.000000 979 92.773000 2331 3006 1 chr6B.!!$F1 675
10 TraesCS5B01G072000 chr4B 623050581 623051257 676 True 994.000000 994 93.205000 2331 3006 1 chr4B.!!$R2 675
11 TraesCS5B01G072000 chr7B 102921032 102921708 676 False 989.000000 989 93.068000 2331 3006 1 chr7B.!!$F1 675
12 TraesCS5B01G072000 chr7B 661495530 661496203 673 False 989.000000 989 93.175000 2331 3003 1 chr7B.!!$F3 672
13 TraesCS5B01G072000 chr7B 444834405 444835081 676 True 983.000000 983 92.910000 2331 3006 1 chr7B.!!$R1 675
14 TraesCS5B01G072000 chr3B 493685026 493685693 667 False 985.000000 985 93.274000 2339 3006 1 chr3B.!!$F1 667

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
915 1553 0.038744 ATGCCTCCTGTTTCCACCTG 59.961 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 2913 0.038251 TGATGTGTCGCCTCAGTGTC 60.038 55.0 0.0 0.0 0.0 3.67 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
23 24 5.277857 TCGGAAGGATCCAATCTAGAAAC 57.722 43.478 15.82 0.00 46.97 2.78
24 25 4.714802 TCGGAAGGATCCAATCTAGAAACA 59.285 41.667 15.82 0.00 46.97 2.83
25 26 4.811557 CGGAAGGATCCAATCTAGAAACAC 59.188 45.833 15.82 0.00 46.97 3.32
26 27 4.811557 GGAAGGATCCAATCTAGAAACACG 59.188 45.833 15.82 0.00 45.79 4.49
27 28 5.395324 GGAAGGATCCAATCTAGAAACACGA 60.395 44.000 15.82 0.00 45.79 4.35
28 29 5.269505 AGGATCCAATCTAGAAACACGAG 57.730 43.478 15.82 0.00 0.00 4.18
29 30 4.956700 AGGATCCAATCTAGAAACACGAGA 59.043 41.667 15.82 0.00 34.98 4.04
30 31 5.068460 AGGATCCAATCTAGAAACACGAGAG 59.932 44.000 15.82 0.00 34.07 3.20
31 32 4.111375 TCCAATCTAGAAACACGAGAGC 57.889 45.455 0.00 0.00 34.07 4.09
32 33 2.854777 CCAATCTAGAAACACGAGAGCG 59.145 50.000 0.00 0.00 44.79 5.03
62 63 2.609491 CGACGACAAGATCCACCAAAGA 60.609 50.000 0.00 0.00 0.00 2.52
68 69 4.583871 ACAAGATCCACCAAAGACAGATC 58.416 43.478 0.00 0.00 34.79 2.75
72 73 4.290722 AGATCCACCAAAGACAGATCCTTT 59.709 41.667 0.00 0.00 35.08 3.11
89 90 2.421388 CCTTTGAAGACACACCTCCACA 60.421 50.000 0.00 0.00 0.00 4.17
96 97 1.973281 CACACCTCCACATGCCCAC 60.973 63.158 0.00 0.00 0.00 4.61
97 98 2.361610 CACCTCCACATGCCCACC 60.362 66.667 0.00 0.00 0.00 4.61
100 101 1.978617 CCTCCACATGCCCACCAAC 60.979 63.158 0.00 0.00 0.00 3.77
110 111 1.090052 GCCCACCAACGATGCTAGAC 61.090 60.000 0.00 0.00 0.00 2.59
120 121 2.986979 TGCTAGACGCACCACCGA 60.987 61.111 0.00 0.00 45.47 4.69
180 182 2.399611 CGTTGCCGCCTCGATTTC 59.600 61.111 0.00 0.00 0.00 2.17
182 184 2.437716 TTGCCGCCTCGATTTCCC 60.438 61.111 0.00 0.00 0.00 3.97
183 185 4.830765 TGCCGCCTCGATTTCCCG 62.831 66.667 0.00 0.00 0.00 5.14
202 204 2.615493 CCGAGCAAGACACAAACCCTAT 60.615 50.000 0.00 0.00 0.00 2.57
205 207 4.072131 GAGCAAGACACAAACCCTATCAA 58.928 43.478 0.00 0.00 0.00 2.57
233 235 5.065988 TCAAAGAAACATATAAAGCCGGAGC 59.934 40.000 5.05 0.00 40.32 4.70
234 236 3.477530 AGAAACATATAAAGCCGGAGCC 58.522 45.455 5.05 0.00 41.25 4.70
240 242 2.397413 ATAAAGCCGGAGCCATCCCG 62.397 60.000 5.05 0.00 43.39 5.14
261 263 1.749258 GGCAAAGACCGGGATCCAC 60.749 63.158 15.23 1.85 0.00 4.02
325 327 3.573491 GCAACGCCTATGGGACGC 61.573 66.667 0.00 0.00 36.24 5.19
338 340 1.695242 TGGGACGCAGAAGAAACCTAA 59.305 47.619 0.00 0.00 0.00 2.69
344 346 5.873164 GGACGCAGAAGAAACCTAATCTTTA 59.127 40.000 0.00 0.00 37.26 1.85
421 424 5.877564 TCAATGTTTGTGTGTCTACAGTTGA 59.122 36.000 0.00 0.00 37.52 3.18
453 456 6.017026 CCAATCTACGCTTCTCTACATAGACA 60.017 42.308 0.00 0.00 0.00 3.41
454 457 6.795098 ATCTACGCTTCTCTACATAGACAG 57.205 41.667 0.00 0.00 0.00 3.51
455 458 5.672503 TCTACGCTTCTCTACATAGACAGT 58.327 41.667 0.00 0.00 0.00 3.55
460 463 7.046652 ACGCTTCTCTACATAGACAGTAGTTA 58.953 38.462 0.00 0.00 39.86 2.24
481 485 3.347216 ACTGTTATGTGCATTGGTCCTC 58.653 45.455 0.00 0.00 0.00 3.71
506 510 4.383444 GGGGTCTTAGCACGGTAACTTAAT 60.383 45.833 0.00 0.00 0.00 1.40
544 554 1.538047 ATTTTGCACGGCTCTGATGT 58.462 45.000 0.00 0.00 0.00 3.06
561 571 2.359354 TTGGGGGCAATGACGACG 60.359 61.111 0.00 0.00 0.00 5.12
571 581 3.296628 GCAATGACGACGTCACATTTTT 58.703 40.909 31.34 18.80 45.65 1.94
574 584 1.003331 TGACGACGTCACATTTTTGGC 60.003 47.619 26.04 0.00 37.67 4.52
576 586 1.673920 ACGACGTCACATTTTTGGCTT 59.326 42.857 17.16 0.00 0.00 4.35
579 589 1.135915 ACGTCACATTTTTGGCTTGCA 59.864 42.857 0.00 0.00 0.00 4.08
582 592 0.860533 CACATTTTTGGCTTGCACCG 59.139 50.000 0.00 0.00 0.00 4.94
597 607 2.887783 TGCACCGGTGTTTGTAATCATT 59.112 40.909 33.92 0.00 0.00 2.57
605 615 6.083630 CGGTGTTTGTAATCATTGTTAGGTG 58.916 40.000 0.00 0.00 0.00 4.00
606 616 6.072948 CGGTGTTTGTAATCATTGTTAGGTGA 60.073 38.462 0.00 0.00 0.00 4.02
607 617 7.081976 GGTGTTTGTAATCATTGTTAGGTGAC 58.918 38.462 0.00 0.00 0.00 3.67
615 625 4.028131 TCATTGTTAGGTGACCTACGGAT 58.972 43.478 11.63 2.58 35.63 4.18
624 634 1.548719 TGACCTACGGATCAGGTTGTG 59.451 52.381 4.80 0.00 46.60 3.33
636 647 7.773224 ACGGATCAGGTTGTGATTTTTATATCA 59.227 33.333 0.00 0.00 46.64 2.15
638 649 9.125026 GGATCAGGTTGTGATTTTTATATCAGT 57.875 33.333 0.00 0.00 46.64 3.41
678 691 6.709018 TTACTGATGATGAATAGACCGACA 57.291 37.500 0.00 0.00 0.00 4.35
682 695 4.811024 TGATGATGAATAGACCGACAAAGC 59.189 41.667 0.00 0.00 0.00 3.51
758 1008 1.535462 CACTGTTTAAGGCGGGTTGAG 59.465 52.381 0.00 0.00 0.00 3.02
815 1433 8.667987 TCTGAATTGTTTATGTTAATTCGTGC 57.332 30.769 0.00 0.00 41.42 5.34
834 1452 1.075748 GGAAATGGCCAGGCTGGAT 60.076 57.895 37.07 19.57 40.96 3.41
851 1489 3.316283 TGGATTTTCAATTGTTCAGCGC 58.684 40.909 0.00 0.00 0.00 5.92
868 1506 2.719774 GCGCGGCAAATTTGAGCAC 61.720 57.895 27.00 19.15 34.53 4.40
891 1529 2.916502 TACGATTGCGCGGATTGCCT 62.917 55.000 8.83 0.00 42.08 4.75
899 1537 3.113745 CGGATTGCCTGACCATGC 58.886 61.111 0.00 0.00 0.00 4.06
915 1553 0.038744 ATGCCTCCTGTTTCCACCTG 59.961 55.000 0.00 0.00 0.00 4.00
979 1617 2.042831 GCTGATGCCCACCAGTGAC 61.043 63.158 0.00 0.00 33.19 3.67
1413 2053 4.395583 GTCGTCGCCGTCTCCGTT 62.396 66.667 0.00 0.00 35.01 4.44
1854 2503 2.356313 CGGCGAGCACTTGTCACT 60.356 61.111 0.00 0.00 0.00 3.41
2021 2670 3.237741 GGCGGAGAGGGAGATGGG 61.238 72.222 0.00 0.00 0.00 4.00
2042 2691 1.134530 GCCGTCGTCTCGTTCATCAG 61.135 60.000 0.00 0.00 0.00 2.90
2078 2727 5.880054 AGGAAATGAAACGATCGATGTTT 57.120 34.783 24.34 19.21 41.94 2.83
2082 2731 4.600012 ATGAAACGATCGATGTTTGGTC 57.400 40.909 24.34 3.75 39.51 4.02
2152 2805 2.559698 TTTGCTCAGATTGTTCCCGA 57.440 45.000 0.00 0.00 0.00 5.14
2153 2806 2.559698 TTGCTCAGATTGTTCCCGAA 57.440 45.000 0.00 0.00 0.00 4.30
2167 2820 5.719173 TGTTCCCGAATTTTCCAAATCATC 58.281 37.500 0.00 0.00 0.00 2.92
2168 2821 4.630894 TCCCGAATTTTCCAAATCATCG 57.369 40.909 0.00 0.00 0.00 3.84
2169 2822 4.013728 TCCCGAATTTTCCAAATCATCGT 58.986 39.130 0.00 0.00 0.00 3.73
2170 2823 4.461081 TCCCGAATTTTCCAAATCATCGTT 59.539 37.500 0.00 0.00 0.00 3.85
2171 2824 4.798387 CCCGAATTTTCCAAATCATCGTTC 59.202 41.667 0.00 0.00 0.00 3.95
2172 2825 4.798387 CCGAATTTTCCAAATCATCGTTCC 59.202 41.667 0.00 0.00 0.00 3.62
2173 2826 5.393027 CCGAATTTTCCAAATCATCGTTCCT 60.393 40.000 0.00 0.00 0.00 3.36
2174 2827 6.092748 CGAATTTTCCAAATCATCGTTCCTT 58.907 36.000 0.00 0.00 0.00 3.36
2177 2830 6.398234 TTTTCCAAATCATCGTTCCTTTGA 57.602 33.333 0.00 0.00 31.76 2.69
2190 2843 4.074970 GTTCCTTTGATCCTTTCTGCTCA 58.925 43.478 0.00 0.00 0.00 4.26
2192 2845 4.927049 TCCTTTGATCCTTTCTGCTCATT 58.073 39.130 0.00 0.00 0.00 2.57
2209 2862 2.026915 TCATTTGCTTGAGCTAGGAGCA 60.027 45.455 12.57 12.57 45.56 4.26
2238 2891 5.534207 TCTGTTGTTGGCTTCAATGATTT 57.466 34.783 0.00 0.00 32.47 2.17
2239 2892 5.916318 TCTGTTGTTGGCTTCAATGATTTT 58.084 33.333 0.00 0.00 32.47 1.82
2240 2893 5.754406 TCTGTTGTTGGCTTCAATGATTTTG 59.246 36.000 0.00 0.00 32.47 2.44
2242 2895 5.879223 TGTTGTTGGCTTCAATGATTTTGTT 59.121 32.000 0.00 0.00 32.47 2.83
2272 3003 0.671796 TTTTCGAGACACTGAGGCGA 59.328 50.000 0.00 0.00 0.00 5.54
2273 3004 0.039437 TTTCGAGACACTGAGGCGAC 60.039 55.000 0.00 0.00 0.00 5.19
2275 3006 1.442857 CGAGACACTGAGGCGACAC 60.443 63.158 0.00 0.00 0.00 3.67
2284 3015 2.200067 CTGAGGCGACACATCATCTTC 58.800 52.381 0.00 0.00 0.00 2.87
2286 3017 1.929836 GAGGCGACACATCATCTTCAC 59.070 52.381 0.00 0.00 0.00 3.18
2290 3021 3.871006 GGCGACACATCATCTTCACATTA 59.129 43.478 0.00 0.00 0.00 1.90
2292 3023 5.258622 GCGACACATCATCTTCACATTAAC 58.741 41.667 0.00 0.00 0.00 2.01
2296 3027 7.433708 ACACATCATCTTCACATTAACGAAA 57.566 32.000 0.00 0.00 0.00 3.46
2298 3029 8.514594 ACACATCATCTTCACATTAACGAAATT 58.485 29.630 0.00 0.00 0.00 1.82
2301 3032 9.345517 CATCATCTTCACATTAACGAAATTGTT 57.654 29.630 0.00 0.00 35.86 2.83
2324 3055 9.256477 TGTTACATAAGTCTTTGTAGTCAACAG 57.744 33.333 0.00 0.00 39.87 3.16
2328 3059 7.441458 ACATAAGTCTTTGTAGTCAACAGGAAC 59.559 37.037 0.00 0.00 39.87 3.62
2329 3060 4.369182 AGTCTTTGTAGTCAACAGGAACG 58.631 43.478 0.00 0.00 39.87 3.95
2337 3068 2.004017 GTCAACAGGAACGTTGTGTCA 58.996 47.619 5.00 0.00 45.28 3.58
2358 3089 5.865552 GTCAGCATGCTTTGTCACATATTTT 59.134 36.000 19.98 0.00 34.76 1.82
2438 4088 8.037758 ACATCCACTTGTTGTTTTGATTGTTTA 58.962 29.630 0.00 0.00 0.00 2.01
2500 4220 7.120726 GCCTAAGAACCTTCTCTAGCTATCTAG 59.879 44.444 0.00 0.00 42.87 2.43
2621 4348 7.647907 TCGTCATAGACTTAAACTTCCAAAC 57.352 36.000 0.00 0.00 0.00 2.93
2622 4349 7.439381 TCGTCATAGACTTAAACTTCCAAACT 58.561 34.615 0.00 0.00 0.00 2.66
2664 4392 1.526887 CCGATTCATCCATTTCGGTCG 59.473 52.381 2.18 0.00 44.65 4.79
2715 4443 2.609002 TCAATCTCGATGCAACCGATTG 59.391 45.455 19.18 19.18 41.21 2.67
2721 4449 1.202065 CGATGCAACCGATTGGAACTG 60.202 52.381 5.81 1.11 39.86 3.16
2726 4454 0.872388 AACCGATTGGAACTGTTCGC 59.128 50.000 13.89 8.00 39.21 4.70
2799 4637 1.331399 TGTTCCACTCGGTCACACCA 61.331 55.000 0.00 0.00 38.47 4.17
3008 5039 1.484653 TCGCTGCATTAGGGTATGTGT 59.515 47.619 0.00 0.00 40.10 3.72
3010 5041 1.867233 GCTGCATTAGGGTATGTGTCG 59.133 52.381 0.00 0.00 0.00 4.35
3011 5042 2.483876 CTGCATTAGGGTATGTGTCGG 58.516 52.381 0.00 0.00 0.00 4.79
3013 5044 1.497991 CATTAGGGTATGTGTCGGCG 58.502 55.000 0.00 0.00 0.00 6.46
3016 5047 0.457035 TAGGGTATGTGTCGGCGTTC 59.543 55.000 6.85 2.07 0.00 3.95
3018 5049 1.082117 GGGTATGTGTCGGCGTTCTG 61.082 60.000 6.85 0.00 0.00 3.02
3020 5051 0.713883 GTATGTGTCGGCGTTCTGTG 59.286 55.000 6.85 0.00 0.00 3.66
3021 5052 0.599060 TATGTGTCGGCGTTCTGTGA 59.401 50.000 6.85 0.00 0.00 3.58
3022 5053 0.249699 ATGTGTCGGCGTTCTGTGAA 60.250 50.000 6.85 0.00 0.00 3.18
3024 5055 1.947146 TGTCGGCGTTCTGTGAACG 60.947 57.895 23.16 23.16 45.56 3.95
3025 5056 2.355363 TCGGCGTTCTGTGAACGG 60.355 61.111 26.64 15.38 43.25 4.44
3026 5057 3.411351 CGGCGTTCTGTGAACGGG 61.411 66.667 26.64 7.67 43.25 5.28
3027 5058 3.047877 GGCGTTCTGTGAACGGGG 61.048 66.667 26.64 7.08 43.25 5.73
3028 5059 3.047877 GCGTTCTGTGAACGGGGG 61.048 66.667 26.64 6.78 43.25 5.40
3029 5060 2.424302 CGTTCTGTGAACGGGGGT 59.576 61.111 20.74 0.00 39.73 4.95
3030 5061 1.666872 CGTTCTGTGAACGGGGGTC 60.667 63.158 20.74 0.00 39.73 4.46
3031 5062 1.302271 GTTCTGTGAACGGGGGTCC 60.302 63.158 0.00 0.00 0.00 4.46
3032 5063 2.522367 TTCTGTGAACGGGGGTCCC 61.522 63.158 0.00 0.00 41.09 4.46
3042 5073 4.048470 GGGGTCCCCAGACTTGCC 62.048 72.222 23.53 0.00 44.65 4.52
3043 5074 2.936032 GGGTCCCCAGACTTGCCT 60.936 66.667 0.00 0.00 43.05 4.75
3044 5075 2.352805 GGTCCCCAGACTTGCCTG 59.647 66.667 0.00 0.00 43.05 4.85
3045 5076 2.360475 GTCCCCAGACTTGCCTGC 60.360 66.667 0.00 0.00 40.10 4.85
3046 5077 3.650950 TCCCCAGACTTGCCTGCC 61.651 66.667 0.00 0.00 32.97 4.85
3047 5078 3.655211 CCCCAGACTTGCCTGCCT 61.655 66.667 0.00 0.00 32.97 4.75
3048 5079 2.360852 CCCAGACTTGCCTGCCTG 60.361 66.667 0.00 0.00 32.97 4.85
3049 5080 3.060615 CCAGACTTGCCTGCCTGC 61.061 66.667 0.00 0.00 32.97 4.85
3050 5081 3.429141 CAGACTTGCCTGCCTGCG 61.429 66.667 0.00 0.00 0.00 5.18
3051 5082 4.711949 AGACTTGCCTGCCTGCGG 62.712 66.667 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.714802 TGTTTCTAGATTGGATCCTTCCGA 59.285 41.667 14.23 6.97 45.89 4.55
2 3 4.811557 GTGTTTCTAGATTGGATCCTTCCG 59.188 45.833 14.23 4.87 45.89 4.30
3 4 4.811557 CGTGTTTCTAGATTGGATCCTTCC 59.188 45.833 14.23 1.48 42.94 3.46
7 8 5.263968 TCTCGTGTTTCTAGATTGGATCC 57.736 43.478 4.20 4.20 0.00 3.36
8 9 4.742659 GCTCTCGTGTTTCTAGATTGGATC 59.257 45.833 0.00 0.00 0.00 3.36
9 10 4.688021 GCTCTCGTGTTTCTAGATTGGAT 58.312 43.478 0.00 0.00 0.00 3.41
10 11 3.427638 CGCTCTCGTGTTTCTAGATTGGA 60.428 47.826 0.00 0.00 0.00 3.53
11 12 2.854777 CGCTCTCGTGTTTCTAGATTGG 59.145 50.000 0.00 0.00 0.00 3.16
25 26 0.583568 GTCGTTCGTCTACGCTCTCG 60.584 60.000 0.00 0.78 41.16 4.04
26 27 0.583568 CGTCGTTCGTCTACGCTCTC 60.584 60.000 0.00 0.00 41.16 3.20
27 28 1.010935 TCGTCGTTCGTCTACGCTCT 61.011 55.000 0.00 0.00 41.16 4.09
28 29 0.851198 GTCGTCGTTCGTCTACGCTC 60.851 60.000 0.00 0.00 41.16 5.03
29 30 1.131420 GTCGTCGTTCGTCTACGCT 59.869 57.895 0.00 0.00 41.16 5.07
30 31 0.722469 TTGTCGTCGTTCGTCTACGC 60.722 55.000 0.00 0.00 41.16 4.42
31 32 1.136529 TCTTGTCGTCGTTCGTCTACG 60.137 52.381 0.00 0.00 42.68 3.51
32 33 2.584166 TCTTGTCGTCGTTCGTCTAC 57.416 50.000 0.00 0.00 40.80 2.59
37 38 0.982673 GTGGATCTTGTCGTCGTTCG 59.017 55.000 0.00 0.00 41.41 3.95
48 49 3.848975 AGGATCTGTCTTTGGTGGATCTT 59.151 43.478 0.00 0.00 34.83 2.40
62 63 3.392616 AGGTGTGTCTTCAAAGGATCTGT 59.607 43.478 0.00 0.00 0.00 3.41
68 69 2.222027 GTGGAGGTGTGTCTTCAAAGG 58.778 52.381 0.00 0.00 0.00 3.11
72 73 1.543208 GCATGTGGAGGTGTGTCTTCA 60.543 52.381 0.00 0.00 0.00 3.02
74 75 0.250901 GGCATGTGGAGGTGTGTCTT 60.251 55.000 0.00 0.00 0.00 3.01
89 90 0.464373 CTAGCATCGTTGGTGGGCAT 60.464 55.000 8.40 0.00 34.79 4.40
131 132 1.479323 TGGAATAAGGTTCCCTCGTCG 59.521 52.381 4.50 0.00 37.79 5.12
134 135 3.388024 TGAGATGGAATAAGGTTCCCTCG 59.612 47.826 4.50 0.00 37.99 4.63
136 137 3.718956 CCTGAGATGGAATAAGGTTCCCT 59.281 47.826 4.50 0.00 37.79 4.20
137 138 3.181439 CCCTGAGATGGAATAAGGTTCCC 60.181 52.174 4.50 0.00 37.79 3.97
149 150 1.153289 CAACGGCTCCCTGAGATGG 60.153 63.158 0.00 0.00 0.00 3.51
176 178 2.270352 TTGTGTCTTGCTCGGGAAAT 57.730 45.000 0.00 0.00 0.00 2.17
180 182 1.515521 GGGTTTGTGTCTTGCTCGGG 61.516 60.000 0.00 0.00 0.00 5.14
182 184 2.163818 TAGGGTTTGTGTCTTGCTCG 57.836 50.000 0.00 0.00 0.00 5.03
183 185 3.674997 TGATAGGGTTTGTGTCTTGCTC 58.325 45.455 0.00 0.00 0.00 4.26
202 204 9.691362 GGCTTTATATGTTTCTTTGAGTTTTGA 57.309 29.630 0.00 0.00 0.00 2.69
205 207 7.175990 TCCGGCTTTATATGTTTCTTTGAGTTT 59.824 33.333 0.00 0.00 0.00 2.66
233 235 2.106683 GTCTTTGCCGACGGGATGG 61.107 63.158 17.22 8.81 34.06 3.51
234 236 2.106683 GGTCTTTGCCGACGGGATG 61.107 63.158 17.22 9.22 34.75 3.51
275 277 1.143277 TCGTCTCCTCTAGCCTTAGGG 59.857 57.143 0.00 0.00 33.40 3.53
283 285 1.146485 TCCGCCTCGTCTCCTCTAG 59.854 63.158 0.00 0.00 0.00 2.43
312 314 1.592669 CTTCTGCGTCCCATAGGCG 60.593 63.158 0.00 0.00 42.00 5.52
323 325 6.969828 AGTAAAGATTAGGTTTCTTCTGCG 57.030 37.500 0.00 0.00 32.33 5.18
325 327 9.810545 CTCCTAGTAAAGATTAGGTTTCTTCTG 57.189 37.037 0.00 0.00 36.60 3.02
338 340 4.884961 TCTTGCCTCCTCCTAGTAAAGAT 58.115 43.478 0.00 0.00 0.00 2.40
344 346 0.689412 GCCTCTTGCCTCCTCCTAGT 60.689 60.000 0.00 0.00 0.00 2.57
421 424 4.407296 AGAGAAGCGTAGATTGGAAGGATT 59.593 41.667 0.00 0.00 34.67 3.01
453 456 6.472887 ACCAATGCACATAACAGTAACTACT 58.527 36.000 0.00 0.00 36.90 2.57
454 457 6.183360 GGACCAATGCACATAACAGTAACTAC 60.183 42.308 0.00 0.00 0.00 2.73
455 458 5.878116 GGACCAATGCACATAACAGTAACTA 59.122 40.000 0.00 0.00 0.00 2.24
460 463 3.009473 AGAGGACCAATGCACATAACAGT 59.991 43.478 0.00 0.00 0.00 3.55
466 469 0.033796 CCCAGAGGACCAATGCACAT 60.034 55.000 0.00 0.00 33.47 3.21
481 485 0.899720 TTACCGTGCTAAGACCCCAG 59.100 55.000 0.00 0.00 0.00 4.45
519 523 5.888691 TCAGAGCCGTGCAAAATTTATTA 57.111 34.783 0.00 0.00 0.00 0.98
532 542 2.671070 CCCCAACATCAGAGCCGT 59.329 61.111 0.00 0.00 0.00 5.68
534 544 2.440980 GCCCCCAACATCAGAGCC 60.441 66.667 0.00 0.00 0.00 4.70
544 554 2.359354 CGTCGTCATTGCCCCCAA 60.359 61.111 0.00 0.00 35.01 4.12
561 571 1.866601 GGTGCAAGCCAAAAATGTGAC 59.133 47.619 0.00 0.00 0.00 3.67
571 581 2.441164 AAACACCGGTGCAAGCCA 60.441 55.556 34.26 0.00 0.00 4.75
574 584 2.292016 TGATTACAAACACCGGTGCAAG 59.708 45.455 34.26 24.26 0.00 4.01
576 586 1.968704 TGATTACAAACACCGGTGCA 58.031 45.000 34.26 18.12 0.00 4.57
579 589 5.182380 CCTAACAATGATTACAAACACCGGT 59.818 40.000 0.00 0.00 0.00 5.28
582 592 7.081976 GTCACCTAACAATGATTACAAACACC 58.918 38.462 0.00 0.00 0.00 4.16
636 647 8.220755 TCAGTAATGTTAGTGCAAAGAAAACT 57.779 30.769 0.00 0.00 34.76 2.66
638 649 8.845227 TCATCAGTAATGTTAGTGCAAAGAAAA 58.155 29.630 0.00 0.00 36.68 2.29
653 666 7.147976 TGTCGGTCTATTCATCATCAGTAATG 58.852 38.462 0.00 0.00 36.65 1.90
654 667 7.290110 TGTCGGTCTATTCATCATCAGTAAT 57.710 36.000 0.00 0.00 0.00 1.89
673 686 6.401955 TTTTCTTTGAAAAAGCTTTGTCGG 57.598 33.333 21.64 14.89 0.00 4.79
731 978 0.881796 GCCTTAAACAGTGACCTGCC 59.118 55.000 0.00 0.00 42.81 4.85
732 979 0.517316 CGCCTTAAACAGTGACCTGC 59.483 55.000 0.00 0.00 42.81 4.85
758 1008 3.244526 ACAATCATTTCCCTTTGCAACCC 60.245 43.478 0.00 0.00 0.00 4.11
815 1433 2.916527 ATCCAGCCTGGCCATTTCCG 62.917 60.000 16.57 0.00 37.47 4.30
834 1452 1.127701 GCGCGCTGAACAATTGAAAA 58.872 45.000 26.67 0.00 0.00 2.29
851 1489 2.427765 CGTGCTCAAATTTGCCGCG 61.428 57.895 21.35 21.35 0.00 6.46
857 1495 4.097714 CAATCGTATGCGTGCTCAAATTT 58.902 39.130 2.37 0.00 39.49 1.82
891 1529 0.038166 GGAAACAGGAGGCATGGTCA 59.962 55.000 0.00 0.00 0.00 4.02
899 1537 2.463441 TCCAGGTGGAAACAGGAGG 58.537 57.895 0.00 0.00 44.46 4.30
979 1617 1.287425 GCTCCCGGAGTAAAATCGTG 58.713 55.000 16.09 0.00 31.39 4.35
1260 1900 1.445582 CACGTCCTTCGGCAGGTAC 60.446 63.158 0.00 0.00 44.37 3.34
1281 1921 3.839432 GGGAGCTTCTCGGACCGG 61.839 72.222 15.25 0.00 0.00 5.28
1360 2000 2.263540 GGCGTTGAGGAAGCGGTA 59.736 61.111 0.00 0.00 0.00 4.02
1407 2047 1.139095 GAGGCGGTAGTCAACGGAG 59.861 63.158 0.00 0.00 0.00 4.63
1587 2236 0.752054 CCCTTGTTGCCATGTTGTGT 59.248 50.000 0.00 0.00 0.00 3.72
1642 2291 2.818132 CACCAGCCCCTCGATCTC 59.182 66.667 0.00 0.00 0.00 2.75
1643 2292 3.474570 GCACCAGCCCCTCGATCT 61.475 66.667 0.00 0.00 33.58 2.75
1854 2503 4.314440 GTGTCCAGCTCCGCCACA 62.314 66.667 0.00 0.00 0.00 4.17
2042 2691 0.828677 TTTCCTACCTTAGCTCCGCC 59.171 55.000 0.00 0.00 0.00 6.13
2052 2701 4.730949 TCGATCGTTTCATTTCCTACCT 57.269 40.909 15.94 0.00 0.00 3.08
2053 2702 4.809426 ACATCGATCGTTTCATTTCCTACC 59.191 41.667 15.94 0.00 0.00 3.18
2054 2703 5.968387 ACATCGATCGTTTCATTTCCTAC 57.032 39.130 15.94 0.00 0.00 3.18
2055 2704 6.183360 CCAAACATCGATCGTTTCATTTCCTA 60.183 38.462 15.94 0.00 34.40 2.94
2056 2705 5.391950 CCAAACATCGATCGTTTCATTTCCT 60.392 40.000 15.94 0.00 34.40 3.36
2062 2711 2.739913 GGACCAAACATCGATCGTTTCA 59.260 45.455 15.94 0.00 34.40 2.69
2078 2727 0.608130 CGGTGACAGAAGATGGACCA 59.392 55.000 0.00 0.00 35.99 4.02
2082 2731 1.811266 CGGCGGTGACAGAAGATGG 60.811 63.158 0.00 0.00 0.00 3.51
2152 2805 7.441017 TCAAAGGAACGATGATTTGGAAAATT 58.559 30.769 0.00 0.00 34.25 1.82
2153 2806 6.991938 TCAAAGGAACGATGATTTGGAAAAT 58.008 32.000 0.00 0.00 34.25 1.82
2167 2820 3.077359 AGCAGAAAGGATCAAAGGAACG 58.923 45.455 0.00 0.00 0.00 3.95
2168 2821 4.074970 TGAGCAGAAAGGATCAAAGGAAC 58.925 43.478 0.00 0.00 28.85 3.62
2169 2822 4.371624 TGAGCAGAAAGGATCAAAGGAA 57.628 40.909 0.00 0.00 28.85 3.36
2170 2823 4.581309 ATGAGCAGAAAGGATCAAAGGA 57.419 40.909 0.00 0.00 36.69 3.36
2171 2824 5.408356 CAAATGAGCAGAAAGGATCAAAGG 58.592 41.667 0.00 0.00 36.69 3.11
2172 2825 4.863131 GCAAATGAGCAGAAAGGATCAAAG 59.137 41.667 0.00 0.00 36.69 2.77
2173 2826 4.525487 AGCAAATGAGCAGAAAGGATCAAA 59.475 37.500 0.00 0.00 36.69 2.69
2174 2827 4.084287 AGCAAATGAGCAGAAAGGATCAA 58.916 39.130 0.00 0.00 36.69 2.57
2177 2830 4.084287 TCAAGCAAATGAGCAGAAAGGAT 58.916 39.130 0.00 0.00 36.85 3.24
2190 2843 2.795231 TGCTCCTAGCTCAAGCAAAT 57.205 45.000 13.44 0.00 42.71 2.32
2209 2862 1.767759 AGCCAACAACAGAAGCACTT 58.232 45.000 0.00 0.00 0.00 3.16
2249 2902 3.678072 CGCCTCAGTGTCTCGAAAATAAA 59.322 43.478 0.00 0.00 0.00 1.40
2252 2905 1.272490 TCGCCTCAGTGTCTCGAAAAT 59.728 47.619 0.00 0.00 0.00 1.82
2253 2906 0.671796 TCGCCTCAGTGTCTCGAAAA 59.328 50.000 0.00 0.00 0.00 2.29
2254 2907 0.039437 GTCGCCTCAGTGTCTCGAAA 60.039 55.000 5.31 0.00 0.00 3.46
2255 2908 1.170290 TGTCGCCTCAGTGTCTCGAA 61.170 55.000 5.31 0.00 0.00 3.71
2256 2909 1.599797 TGTCGCCTCAGTGTCTCGA 60.600 57.895 0.00 0.00 0.00 4.04
2258 2911 0.244994 ATGTGTCGCCTCAGTGTCTC 59.755 55.000 0.00 0.00 0.00 3.36
2259 2912 0.244994 GATGTGTCGCCTCAGTGTCT 59.755 55.000 0.00 0.00 0.00 3.41
2260 2913 0.038251 TGATGTGTCGCCTCAGTGTC 60.038 55.000 0.00 0.00 0.00 3.67
2261 2914 0.610174 ATGATGTGTCGCCTCAGTGT 59.390 50.000 0.00 0.00 0.00 3.55
2264 2917 2.200067 GAAGATGATGTGTCGCCTCAG 58.800 52.381 0.00 0.00 0.00 3.35
2266 2919 1.929836 GTGAAGATGATGTGTCGCCTC 59.070 52.381 0.00 0.00 0.00 4.70
2267 2920 1.276138 TGTGAAGATGATGTGTCGCCT 59.724 47.619 0.00 0.00 0.00 5.52
2268 2921 1.725641 TGTGAAGATGATGTGTCGCC 58.274 50.000 0.00 0.00 0.00 5.54
2269 2922 5.258622 GTTAATGTGAAGATGATGTGTCGC 58.741 41.667 0.00 0.00 0.00 5.19
2272 3003 7.433708 TTTCGTTAATGTGAAGATGATGTGT 57.566 32.000 0.00 0.00 0.00 3.72
2273 3004 8.791605 CAATTTCGTTAATGTGAAGATGATGTG 58.208 33.333 0.00 0.00 0.00 3.21
2275 3006 8.900511 ACAATTTCGTTAATGTGAAGATGATG 57.099 30.769 0.00 0.00 0.00 3.07
2298 3029 9.256477 CTGTTGACTACAAAGACTTATGTAACA 57.744 33.333 9.82 10.82 37.77 2.41
2301 3032 8.185506 TCCTGTTGACTACAAAGACTTATGTA 57.814 34.615 8.80 8.80 37.77 2.29
2305 3036 5.981315 CGTTCCTGTTGACTACAAAGACTTA 59.019 40.000 0.00 0.00 37.77 2.24
2306 3037 4.809426 CGTTCCTGTTGACTACAAAGACTT 59.191 41.667 0.00 0.00 37.77 3.01
2307 3038 4.142004 ACGTTCCTGTTGACTACAAAGACT 60.142 41.667 0.00 0.00 37.77 3.24
2320 3051 1.014352 GCTGACACAACGTTCCTGTT 58.986 50.000 0.00 0.00 0.00 3.16
2321 3052 0.107897 TGCTGACACAACGTTCCTGT 60.108 50.000 0.00 2.38 0.00 4.00
2322 3053 1.069703 CATGCTGACACAACGTTCCTG 60.070 52.381 0.00 0.00 0.00 3.86
2324 3055 0.385974 GCATGCTGACACAACGTTCC 60.386 55.000 11.37 0.00 0.00 3.62
2328 3059 1.268692 ACAAAGCATGCTGACACAACG 60.269 47.619 23.48 6.21 0.00 4.10
2329 3060 2.223548 TGACAAAGCATGCTGACACAAC 60.224 45.455 23.48 9.86 0.00 3.32
2337 3068 8.875803 CAAATAAAATATGTGACAAAGCATGCT 58.124 29.630 16.30 16.30 0.00 3.79
2358 3089 6.695429 TGCTCACACAATAAAATGGCAAATA 58.305 32.000 0.00 0.00 0.00 1.40
2438 4088 7.404671 TCTACTTGGCAAAAGAAAAGAAACT 57.595 32.000 0.00 0.00 0.00 2.66
2500 4220 7.920682 TGAATAAAGTTTGAGACAAGAAAAGCC 59.079 33.333 0.00 0.00 0.00 4.35
2621 4348 1.597663 AGACCGAAACGCACAAAGAAG 59.402 47.619 0.00 0.00 0.00 2.85
2622 4349 1.329292 CAGACCGAAACGCACAAAGAA 59.671 47.619 0.00 0.00 0.00 2.52
2715 4443 1.557443 CGGTGTGAGCGAACAGTTCC 61.557 60.000 7.76 1.05 42.41 3.62
2726 4454 2.545952 AGTTACTGCAACTCGGTGTGAG 60.546 50.000 0.00 0.00 44.48 3.51
2799 4637 4.944177 AGTATATATAGCCCGACCCTGTT 58.056 43.478 0.00 0.00 0.00 3.16
2808 4646 4.275810 TGACCCGTGAGTATATATAGCCC 58.724 47.826 0.00 0.00 0.00 5.19
2870 4708 2.354401 CCGAAGAGGCAGAGCAGGA 61.354 63.158 0.00 0.00 0.00 3.86
3008 5039 2.355363 CCGTTCACAGAACGCCGA 60.355 61.111 22.64 0.00 41.85 5.54
3010 5041 3.047877 CCCCGTTCACAGAACGCC 61.048 66.667 22.64 0.00 41.85 5.68
3011 5042 3.047877 CCCCCGTTCACAGAACGC 61.048 66.667 22.64 0.00 41.85 4.84
3013 5044 1.302271 GGACCCCCGTTCACAGAAC 60.302 63.158 0.00 0.00 0.00 3.01
3016 5047 4.029809 GGGGACCCCCGTTCACAG 62.030 72.222 20.38 0.00 46.66 3.66
3028 5059 2.360475 GCAGGCAAGTCTGGGGAC 60.360 66.667 3.62 0.00 42.41 4.46
3029 5060 3.650950 GGCAGGCAAGTCTGGGGA 61.651 66.667 3.62 0.00 35.43 4.81
3030 5061 3.655211 AGGCAGGCAAGTCTGGGG 61.655 66.667 3.62 0.00 35.43 4.96
3031 5062 2.360852 CAGGCAGGCAAGTCTGGG 60.361 66.667 3.62 0.00 37.58 4.45
3032 5063 3.060615 GCAGGCAGGCAAGTCTGG 61.061 66.667 12.46 0.00 41.45 3.86
3033 5064 3.429141 CGCAGGCAGGCAAGTCTG 61.429 66.667 7.14 7.14 43.93 3.51
3034 5065 4.711949 CCGCAGGCAGGCAAGTCT 62.712 66.667 0.00 0.00 46.14 3.24


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

AutoCloner maintained by Alex Coulton.