Multiple sequence alignment - TraesCS7B01G142400

Loading Multiple Alignment...

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 TraesCS7B01G142400 chr7B 100.000 3988 0 0 1 3988 181635623 181631636 0.000000e+00 7365.0
1 TraesCS7B01G142400 chr7B 76.549 226 37 12 285 501 621290490 621290708 4.210000e-20 110.0
2 TraesCS7B01G142400 chr7B 91.429 70 5 1 3578 3647 181631982 181631914 1.180000e-15 95.3
3 TraesCS7B01G142400 chr7B 91.429 70 5 1 3642 3710 181632046 181631977 1.180000e-15 95.3
4 TraesCS7B01G142400 chr7B 75.595 168 33 5 332 498 1096347 1096187 4.270000e-10 76.8
5 TraesCS7B01G142400 chr7D 93.900 2787 100 20 994 3747 218175597 218178346 0.000000e+00 4141.0
6 TraesCS7B01G142400 chr7D 85.138 471 60 8 2 465 218053144 218053611 1.300000e-129 473.0
7 TraesCS7B01G142400 chr7D 91.343 335 14 4 3666 3988 218178347 218178678 1.020000e-120 444.0
8 TraesCS7B01G142400 chr7A 94.413 2309 83 18 1037 3312 230876343 230878638 0.000000e+00 3507.0
9 TraesCS7B01G142400 chr7A 79.477 994 122 38 26 976 230875166 230876120 7.270000e-177 630.0
10 TraesCS7B01G142400 chr7A 77.822 505 82 21 20 499 657683141 657682642 6.520000e-73 285.0
11 TraesCS7B01G142400 chr7A 78.372 430 64 19 1 417 576879459 576879872 6.620000e-63 252.0
12 TraesCS7B01G142400 chr6D 82.653 392 56 11 3257 3642 327723930 327723545 1.780000e-88 337.0
13 TraesCS7B01G142400 chr6D 77.975 395 72 11 3220 3603 369707478 369707868 2.400000e-57 233.0
14 TraesCS7B01G142400 chr1B 78.029 487 82 21 1 466 670526105 670526587 2.350000e-72 283.0
15 TraesCS7B01G142400 chr6B 80.357 392 60 14 3257 3642 491948379 491947999 8.440000e-72 281.0
16 TraesCS7B01G142400 chr3A 77.801 482 86 17 1 466 623828985 623828509 1.090000e-70 278.0
17 TraesCS7B01G142400 chr6A 77.479 484 83 17 1 464 499790425 499789948 2.360000e-67 267.0
18 TraesCS7B01G142400 chr6A 78.281 221 39 8 3720 3932 493752980 493752761 2.500000e-27 134.0
19 TraesCS7B01G142400 chr6A 79.474 190 29 9 355 541 52851379 52851197 4.180000e-25 126.0
20 TraesCS7B01G142400 chr6A 76.882 186 28 12 3226 3397 479881621 479881437 1.530000e-14 91.6
21 TraesCS7B01G142400 chr3B 77.165 508 81 25 1 499 128657391 128657872 3.060000e-66 263.0
22 TraesCS7B01G142400 chr3B 75.381 394 80 13 3220 3603 171100500 171100886 1.470000e-39 174.0
23 TraesCS7B01G142400 chr5D 77.647 425 81 10 3226 3642 508580534 508580952 3.080000e-61 246.0
24 TraesCS7B01G142400 chr5D 82.022 267 35 8 3720 3979 356092721 356092981 8.680000e-52 215.0
25 TraesCS7B01G142400 chr5D 77.778 306 52 8 3644 3936 508580890 508581192 1.470000e-39 174.0
26 TraesCS7B01G142400 chr5D 75.369 203 40 9 221 417 5575002 5575200 5.490000e-14 89.8
27 TraesCS7B01G142400 chr5B 76.701 485 79 19 1 466 429430488 429430957 5.150000e-59 239.0
28 TraesCS7B01G142400 chr4D 76.706 425 82 15 3226 3642 85535547 85535962 1.870000e-53 220.0
29 TraesCS7B01G142400 chr4D 78.116 329 57 12 3644 3966 101056995 101056676 1.130000e-45 195.0
30 TraesCS7B01G142400 chr4D 79.695 197 36 4 200 392 499591031 499590835 5.370000e-29 139.0
31 TraesCS7B01G142400 chr1D 77.519 387 72 14 3267 3642 363060188 363059806 6.710000e-53 219.0
32 TraesCS7B01G142400 chr1A 76.675 403 78 11 2 392 513107456 513107058 4.040000e-50 209.0
33 TraesCS7B01G142400 chr2A 76.903 381 65 16 3220 3591 762724297 762724663 1.130000e-45 195.0
34 TraesCS7B01G142400 chr4B 82.028 217 28 10 229 441 507361362 507361153 1.470000e-39 174.0
35 TraesCS7B01G142400 chr4B 80.000 185 24 9 325 500 37117669 37117489 1.500000e-24 124.0
36 TraesCS7B01G142400 chr4B 78.155 206 31 12 278 478 507361417 507361221 7.000000e-23 119.0
37 TraesCS7B01G142400 chr2D 79.638 221 40 4 3720 3936 616432990 616433209 1.920000e-33 154.0
38 TraesCS7B01G142400 chr2D 79.904 209 28 10 218 417 477226277 477226074 1.490000e-29 141.0
39 TraesCS7B01G142400 chr4A 79.070 215 33 11 308 517 491669017 491668810 1.930000e-28 137.0
40 TraesCS7B01G142400 chr4A 78.613 173 27 9 371 541 546251024 546250860 5.450000e-19 106.0
41 TraesCS7B01G142400 chr4A 71.429 448 95 26 3220 3642 463891867 463891428 1.970000e-13 87.9


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 TraesCS7B01G142400 chr7B 181631636 181635623 3987 True 2518.533333 7365 94.2860 1 3988 3 chr7B.!!$R2 3987
1 TraesCS7B01G142400 chr7D 218175597 218178678 3081 False 2292.500000 4141 92.6215 994 3988 2 chr7D.!!$F2 2994
2 TraesCS7B01G142400 chr7A 230875166 230878638 3472 False 2068.500000 3507 86.9450 26 3312 2 chr7A.!!$F2 3286
3 TraesCS7B01G142400 chr5D 508580534 508581192 658 False 210.000000 246 77.7125 3226 3936 2 chr5D.!!$F3 710

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
927 969 0.029834 GCTGATAGCACGCCAAATGG 59.970 55.0 0.0 0.0 41.89 3.16 F
1471 1678 0.035439 GCAGGTCGATTTCCCCTTGA 60.035 55.0 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2763 2988 0.590195 CTCACAGCAACAAGACCTGC 59.410 55.000 0.00 0.0 38.91 4.85 R
3423 3667 2.086869 CTGGACAATAGTGCACAAGGG 58.913 52.381 21.04 8.3 41.46 3.95 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
20 21 3.354089 CTTGTCGCAACCTGTCATTTT 57.646 42.857 0.00 0.00 0.00 1.82
21 22 3.705604 CTTGTCGCAACCTGTCATTTTT 58.294 40.909 0.00 0.00 0.00 1.94
86 87 5.508200 TTAAACTGTGCGTCCAAATCTTT 57.492 34.783 0.00 0.00 0.00 2.52
89 90 4.483476 ACTGTGCGTCCAAATCTTTAAC 57.517 40.909 0.00 0.00 0.00 2.01
90 91 3.252458 ACTGTGCGTCCAAATCTTTAACC 59.748 43.478 0.00 0.00 0.00 2.85
91 92 2.224549 TGTGCGTCCAAATCTTTAACCG 59.775 45.455 0.00 0.00 0.00 4.44
100 101 6.304683 GTCCAAATCTTTAACCGTTTTCATCG 59.695 38.462 0.00 0.00 0.00 3.84
101 102 5.060446 CCAAATCTTTAACCGTTTTCATCGC 59.940 40.000 0.00 0.00 0.00 4.58
144 145 8.440771 AGATATTTAAAACTAGATCCCAGGTGG 58.559 37.037 0.00 0.00 0.00 4.61
162 163 5.872617 CAGGTGGATATGTTTTGACGAACTA 59.127 40.000 0.00 0.00 0.00 2.24
180 181 8.389586 ACGAACTATTTTCTTCACACAAAAAC 57.610 30.769 0.00 0.00 0.00 2.43
181 182 7.217447 ACGAACTATTTTCTTCACACAAAAACG 59.783 33.333 0.00 0.00 0.00 3.60
182 183 7.305190 CGAACTATTTTCTTCACACAAAAACGG 60.305 37.037 0.00 0.00 0.00 4.44
184 185 6.970613 ACTATTTTCTTCACACAAAAACGGAC 59.029 34.615 0.00 0.00 0.00 4.79
185 186 3.392769 TTCTTCACACAAAAACGGACG 57.607 42.857 0.00 0.00 0.00 4.79
270 273 0.807496 GCCTCTCGCAGAAGCAAATT 59.193 50.000 2.95 0.00 42.27 1.82
281 284 2.036346 AGAAGCAAATTTGTGCCTCCAC 59.964 45.455 19.03 0.45 46.14 4.02
282 285 0.314935 AGCAAATTTGTGCCTCCACG 59.685 50.000 19.03 0.00 46.14 4.94
287 290 1.813513 ATTTGTGCCTCCACGAGAAG 58.186 50.000 0.00 0.00 45.04 2.85
289 292 1.334160 TTGTGCCTCCACGAGAAGTA 58.666 50.000 0.00 0.00 45.04 2.24
293 296 1.689813 TGCCTCCACGAGAAGTAAACA 59.310 47.619 0.00 0.00 0.00 2.83
346 349 1.176619 TCCGTTTCTGAGAGGCACGA 61.177 55.000 11.12 0.00 32.51 4.35
358 361 2.887568 GCACGACCATGCCTCTCG 60.888 66.667 0.00 0.00 39.86 4.04
359 362 2.887568 CACGACCATGCCTCTCGC 60.888 66.667 0.00 0.00 38.31 5.03
364 367 0.809241 GACCATGCCTCTCGCTGAAG 60.809 60.000 0.00 0.00 38.78 3.02
372 375 1.061711 CCTCTCGCTGAAGCAAATTCG 59.938 52.381 2.79 0.00 41.14 3.34
382 385 1.226128 GCAAATTCGTGCCTCTCGC 60.226 57.895 0.00 0.00 38.66 5.03
401 404 1.017701 CGGAAGCAAACCCGTACCTC 61.018 60.000 0.00 0.00 40.78 3.85
403 406 1.675116 GGAAGCAAACCCGTACCTCTC 60.675 57.143 0.00 0.00 0.00 3.20
405 408 1.183676 AGCAAACCCGTACCTCTCGT 61.184 55.000 0.00 0.00 0.00 4.18
409 412 1.331214 AACCCGTACCTCTCGTGAAA 58.669 50.000 0.00 0.00 0.00 2.69
451 455 2.196295 TTTCGTTTCCAAAAGGCACG 57.804 45.000 0.00 0.00 0.00 5.34
453 457 0.748729 TCGTTTCCAAAAGGCACGGT 60.749 50.000 0.00 0.00 0.00 4.83
455 459 0.317519 GTTTCCAAAAGGCACGGTCG 60.318 55.000 0.00 0.00 0.00 4.79
479 484 2.662596 TCGCAGAGGCAAATCCGT 59.337 55.556 0.00 0.00 41.24 4.69
481 486 0.464036 TCGCAGAGGCAAATCCGTAT 59.536 50.000 0.00 0.00 41.24 3.06
489 494 2.128035 GGCAAATCCGTATCTCTCACG 58.872 52.381 0.00 0.00 39.10 4.35
490 495 2.223735 GGCAAATCCGTATCTCTCACGA 60.224 50.000 0.00 0.00 41.91 4.35
495 500 5.578005 AATCCGTATCTCTCACGAAAGAA 57.422 39.130 0.00 0.00 41.91 2.52
496 501 5.578005 ATCCGTATCTCTCACGAAAGAAA 57.422 39.130 0.00 0.00 41.91 2.52
497 502 5.381174 TCCGTATCTCTCACGAAAGAAAA 57.619 39.130 0.00 0.00 41.91 2.29
498 503 5.775686 TCCGTATCTCTCACGAAAGAAAAA 58.224 37.500 0.00 0.00 41.91 1.94
523 528 8.825064 AAAAATGCATTTTTCTCGTTTTTCAG 57.175 26.923 34.01 0.00 44.17 3.02
526 531 5.280945 TGCATTTTTCTCGTTTTTCAGGAG 58.719 37.500 0.00 0.00 38.56 3.69
545 550 4.979204 CACGGCCGTGTCTCTTAA 57.021 55.556 42.92 0.00 40.91 1.85
548 553 1.459592 CACGGCCGTGTCTCTTAAAAG 59.540 52.381 42.92 18.83 40.91 2.27
549 554 1.069668 ACGGCCGTGTCTCTTAAAAGT 59.930 47.619 33.75 0.00 0.00 2.66
554 564 4.035909 GGCCGTGTCTCTTAAAAGTGAAAA 59.964 41.667 0.00 0.00 31.18 2.29
647 676 2.018544 TTTTTGACAGACACGGCCG 58.981 52.632 26.86 26.86 0.00 6.13
697 734 2.851263 TTTAGAGGCACGACCATGTT 57.149 45.000 0.00 0.00 43.14 2.71
701 738 1.079503 GAGGCACGACCATGTTTCTC 58.920 55.000 0.00 0.00 43.14 2.87
709 746 0.034896 ACCATGTTTCTCGCGGAAGT 59.965 50.000 6.13 0.04 35.16 3.01
714 751 4.494199 CCATGTTTCTCGCGGAAGTAAATC 60.494 45.833 6.13 0.00 35.16 2.17
727 764 5.437060 GGAAGTAAATCCATACCTCTTGCA 58.563 41.667 0.00 0.00 39.42 4.08
732 769 4.725790 AATCCATACCTCTTGCAAAAGC 57.274 40.909 0.00 0.00 0.00 3.51
742 779 7.622893 ACCTCTTGCAAAAGCAAAAATAAAA 57.377 28.000 0.00 0.00 0.00 1.52
818 856 3.878160 AAAAAGACCGTTCAAAAGCCA 57.122 38.095 0.00 0.00 0.00 4.75
819 857 3.878160 AAAAGACCGTTCAAAAGCCAA 57.122 38.095 0.00 0.00 0.00 4.52
856 894 9.689075 GAAAAACATCTAAAAAGCTGAAAACAC 57.311 29.630 0.00 0.00 0.00 3.32
864 902 6.532365 AAAAAGCTGAAAACACGTGAAAAA 57.468 29.167 25.01 2.54 0.00 1.94
907 949 4.702081 GAGCGACACGTGACGGCT 62.702 66.667 34.04 29.77 34.07 5.52
911 953 3.406361 GACACGTGACGGCTGCTG 61.406 66.667 25.01 6.98 0.00 4.41
912 954 3.841379 GACACGTGACGGCTGCTGA 62.841 63.158 25.01 0.00 0.00 4.26
913 955 2.433145 CACGTGACGGCTGCTGAT 60.433 61.111 16.72 0.00 0.00 2.90
914 956 1.153842 CACGTGACGGCTGCTGATA 60.154 57.895 16.72 0.08 0.00 2.15
915 957 1.139734 ACGTGACGGCTGCTGATAG 59.860 57.895 16.72 6.02 0.00 2.08
927 969 0.029834 GCTGATAGCACGCCAAATGG 59.970 55.000 0.00 0.00 41.89 3.16
939 981 1.353103 CAAATGGCGCGCTCTAAGG 59.647 57.895 32.29 12.70 0.00 2.69
976 1018 0.984961 TGAGGGGCTCCTTCATCAGG 60.985 60.000 6.58 0.00 45.05 3.86
977 1019 2.194326 GGGGCTCCTTCATCAGGC 59.806 66.667 0.00 0.00 43.55 4.85
978 1020 2.381941 GGGGCTCCTTCATCAGGCT 61.382 63.158 0.00 0.00 43.55 4.58
979 1021 1.148048 GGGCTCCTTCATCAGGCTC 59.852 63.158 0.00 0.00 43.55 4.70
980 1022 1.148048 GGCTCCTTCATCAGGCTCC 59.852 63.158 0.00 0.00 43.55 4.70
983 1025 1.765314 GCTCCTTCATCAGGCTCCTTA 59.235 52.381 0.00 0.00 43.55 2.69
984 1026 2.484594 GCTCCTTCATCAGGCTCCTTAC 60.485 54.545 0.00 0.00 43.55 2.34
985 1027 2.768527 CTCCTTCATCAGGCTCCTTACA 59.231 50.000 0.00 0.00 43.55 2.41
988 1030 4.228210 TCCTTCATCAGGCTCCTTACATTT 59.772 41.667 0.00 0.00 43.55 2.32
989 1031 4.578105 CCTTCATCAGGCTCCTTACATTTC 59.422 45.833 0.00 0.00 35.13 2.17
990 1032 5.435291 CTTCATCAGGCTCCTTACATTTCT 58.565 41.667 0.00 0.00 0.00 2.52
991 1033 4.774124 TCATCAGGCTCCTTACATTTCTG 58.226 43.478 0.00 0.00 0.00 3.02
992 1034 4.225942 TCATCAGGCTCCTTACATTTCTGT 59.774 41.667 0.00 0.00 39.49 3.41
1008 1050 6.313905 ACATTTCTGTCTGACCGATACAAATC 59.686 38.462 5.17 0.00 0.00 2.17
1423 1630 0.395311 CGCCTACTACCTCTGGGTCA 60.395 60.000 0.00 0.00 45.98 4.02
1471 1678 0.035439 GCAGGTCGATTTCCCCTTGA 60.035 55.000 0.00 0.00 0.00 3.02
1488 1695 4.638421 CCCTTGATAATTCTTGTTACCGCA 59.362 41.667 0.00 0.00 0.00 5.69
1489 1696 5.448632 CCCTTGATAATTCTTGTTACCGCAC 60.449 44.000 0.00 0.00 0.00 5.34
1493 1709 5.810587 TGATAATTCTTGTTACCGCACTCTC 59.189 40.000 0.00 0.00 0.00 3.20
1494 1710 2.060326 TTCTTGTTACCGCACTCTCG 57.940 50.000 0.00 0.00 0.00 4.04
1541 1757 2.429907 CTCGGATGAGATCGCCGC 60.430 66.667 12.44 0.00 45.57 6.53
1543 1759 2.732468 CGGATGAGATCGCCGCAG 60.732 66.667 6.46 0.00 38.46 5.18
1576 1793 3.074412 CCACATCTCTACAAGCCGTTTT 58.926 45.455 0.00 0.00 0.00 2.43
1666 1883 0.107831 AGGAACTGTGCGTTGGCTTA 59.892 50.000 0.00 0.00 37.18 3.09
1677 1894 1.396996 CGTTGGCTTACTCGGAATTGG 59.603 52.381 0.00 0.00 0.00 3.16
2107 2331 4.964593 TCCTGTAAGACACCCTTGTTTAC 58.035 43.478 0.00 0.00 35.47 2.01
2238 2463 4.203950 TGTCTGTTTTCGTTCCATTTCG 57.796 40.909 0.00 0.00 0.00 3.46
2371 2596 7.164122 CACTCTGTTGATAATGGTATATGCCT 58.836 38.462 11.44 0.00 0.00 4.75
2372 2597 7.663081 CACTCTGTTGATAATGGTATATGCCTT 59.337 37.037 11.44 1.69 0.00 4.35
2373 2598 8.220559 ACTCTGTTGATAATGGTATATGCCTTT 58.779 33.333 11.44 12.93 0.00 3.11
2397 2622 0.319900 TTCACAGGAACGAGCTGCTC 60.320 55.000 19.53 19.53 0.00 4.26
2590 2815 3.914426 CAGGACACTGGCCTAACTTAT 57.086 47.619 1.96 0.00 41.13 1.73
2635 2860 6.568653 CGAAGTCTGACAACTAGTTCATCTGA 60.569 42.308 4.77 12.40 0.00 3.27
2655 2880 5.013079 TCTGAGAACATCCTGTACCAAATGT 59.987 40.000 0.00 0.00 33.92 2.71
2676 2901 2.560542 TGGCATTCGTTTAACTGGCAAT 59.439 40.909 9.04 0.00 40.65 3.56
2759 2984 1.912043 AGGTTGCTTCCTCATGCTAGT 59.088 47.619 0.00 0.00 31.32 2.57
2763 2988 3.827008 TGCTTCCTCATGCTAGTAAGG 57.173 47.619 0.00 0.00 0.00 2.69
2776 3001 1.897560 AGTAAGGCAGGTCTTGTTGC 58.102 50.000 0.00 0.00 39.56 4.17
2777 3002 1.421646 AGTAAGGCAGGTCTTGTTGCT 59.578 47.619 0.00 0.00 40.15 3.91
2799 3026 4.112634 TGTGAGTCTCTTCGTTTTGAGTG 58.887 43.478 0.65 0.00 0.00 3.51
3064 3301 1.659098 CGATTACAGAAGTGCCGGAAC 59.341 52.381 5.05 4.25 0.00 3.62
3144 3381 5.899547 AGAGAGATGGAATGTACACATACCA 59.100 40.000 0.00 6.17 35.10 3.25
3145 3382 6.041409 AGAGAGATGGAATGTACACATACCAG 59.959 42.308 0.00 0.00 35.10 4.00
3146 3383 5.899547 AGAGATGGAATGTACACATACCAGA 59.100 40.000 0.00 0.00 35.10 3.86
3147 3384 6.556495 AGAGATGGAATGTACACATACCAGAT 59.444 38.462 0.00 0.00 35.10 2.90
3148 3385 7.730332 AGAGATGGAATGTACACATACCAGATA 59.270 37.037 0.00 0.00 35.10 1.98
3149 3386 7.671302 AGATGGAATGTACACATACCAGATAC 58.329 38.462 0.00 0.66 35.10 2.24
3150 3387 6.800072 TGGAATGTACACATACCAGATACA 57.200 37.500 0.00 0.00 35.10 2.29
3151 3388 6.578944 TGGAATGTACACATACCAGATACAC 58.421 40.000 0.00 0.00 35.10 2.90
3187 3428 5.536161 TCTTTCAAAGGCTGAGCTACAATTT 59.464 36.000 3.72 0.00 34.81 1.82
3345 3589 2.026905 GCCTTCACCACCCAGAAACAA 61.027 52.381 0.00 0.00 0.00 2.83
3423 3667 1.608801 CCCAAGCCAACAAATCCAAGC 60.609 52.381 0.00 0.00 0.00 4.01
3539 3783 1.608025 GGTGGACTTCGACATGCTTGA 60.608 52.381 6.60 0.00 0.00 3.02
3587 3831 2.056481 GACGGCCTCATTCATGCTGC 62.056 60.000 0.00 0.00 34.72 5.25
3604 3848 2.351157 GCTGCGAAAGATGTTGAGCTTT 60.351 45.455 0.00 0.00 40.54 3.51
3610 3854 4.676924 CGAAAGATGTTGAGCTTTTTGTCC 59.323 41.667 0.00 0.00 37.93 4.02
3614 3858 4.828939 AGATGTTGAGCTTTTTGTCCATCA 59.171 37.500 0.00 0.00 32.02 3.07
3650 3894 7.290948 TCTTCCTCTTCCTATCAATTCATGCTA 59.709 37.037 0.00 0.00 0.00 3.49
3698 4027 5.213868 TCATACCTCTCCTCTTCCTCTTT 57.786 43.478 0.00 0.00 0.00 2.52
3701 4030 3.440127 ACCTCTCCTCTTCCTCTTTCTG 58.560 50.000 0.00 0.00 0.00 3.02
3818 4157 1.357420 TGGAGCCCATGGTATGTTTGT 59.643 47.619 11.73 0.00 0.00 2.83
3862 4201 2.073117 TTCGTTGCATCTGCGAGTAA 57.927 45.000 0.00 0.00 45.83 2.24
3863 4202 1.346365 TCGTTGCATCTGCGAGTAAC 58.654 50.000 0.00 0.00 45.83 2.50
3936 4278 6.262273 AGAAACACAGTATGGTTAGTTTGTGG 59.738 38.462 7.26 0.00 38.80 4.17
3953 4295 3.411446 TGTGGTTGGCATGTTAGAGAAG 58.589 45.455 0.00 0.00 0.00 2.85
3968 4310 6.540914 TGTTAGAGAAGGTTAAACAAGTGGTG 59.459 38.462 0.00 0.00 0.00 4.17
3970 4312 4.881850 AGAGAAGGTTAAACAAGTGGTGTG 59.118 41.667 0.00 0.00 40.60 3.82
3981 4323 2.802816 CAAGTGGTGTGTGAGCTAAGAC 59.197 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.354089 AAAATGACAGGTTGCGACAAG 57.646 42.857 6.39 0.00 0.00 3.16
1 2 3.791973 AAAAATGACAGGTTGCGACAA 57.208 38.095 6.39 0.00 0.00 3.18
53 54 7.012515 TGGACGCACAGTTTAAAAGATAAAAGA 59.987 33.333 0.00 0.00 0.00 2.52
55 56 7.028926 TGGACGCACAGTTTAAAAGATAAAA 57.971 32.000 0.00 0.00 0.00 1.52
75 76 6.304683 CGATGAAAACGGTTAAAGATTTGGAC 59.695 38.462 0.00 0.00 0.00 4.02
86 87 2.459060 TCCAGCGATGAAAACGGTTA 57.541 45.000 0.06 0.00 40.88 2.85
89 90 1.064060 GGAATCCAGCGATGAAAACGG 59.936 52.381 0.06 0.00 30.42 4.44
90 91 2.009774 AGGAATCCAGCGATGAAAACG 58.990 47.619 0.06 0.00 34.14 3.60
91 92 2.030946 CGAGGAATCCAGCGATGAAAAC 59.969 50.000 0.06 0.00 0.00 2.43
100 101 1.424493 CTCAACGCGAGGAATCCAGC 61.424 60.000 15.93 5.85 38.18 4.85
101 102 0.173481 TCTCAACGCGAGGAATCCAG 59.827 55.000 15.93 0.00 42.55 3.86
122 123 6.652205 TCCACCTGGGATCTAGTTTTAAAT 57.348 37.500 0.00 0.00 42.15 1.40
140 141 6.920569 ATAGTTCGTCAAAACATATCCACC 57.079 37.500 0.00 0.00 0.00 4.61
162 163 4.796312 CGTCCGTTTTTGTGTGAAGAAAAT 59.204 37.500 0.00 0.00 0.00 1.82
226 229 3.131396 GTCACGCCTCTTTCAGAAAGAA 58.869 45.455 23.16 7.66 46.13 2.52
227 230 2.365617 AGTCACGCCTCTTTCAGAAAGA 59.634 45.455 21.96 21.96 44.82 2.52
228 231 2.478134 CAGTCACGCCTCTTTCAGAAAG 59.522 50.000 15.89 15.89 39.88 2.62
231 234 1.040646 ACAGTCACGCCTCTTTCAGA 58.959 50.000 0.00 0.00 0.00 3.27
232 235 1.143305 CACAGTCACGCCTCTTTCAG 58.857 55.000 0.00 0.00 0.00 3.02
233 236 0.880278 GCACAGTCACGCCTCTTTCA 60.880 55.000 0.00 0.00 0.00 2.69
234 237 1.569479 GGCACAGTCACGCCTCTTTC 61.569 60.000 0.00 0.00 45.29 2.62
235 238 1.598130 GGCACAGTCACGCCTCTTT 60.598 57.895 0.00 0.00 45.29 2.52
236 239 2.031163 GGCACAGTCACGCCTCTT 59.969 61.111 0.00 0.00 45.29 2.85
241 244 2.807045 CGAGAGGCACAGTCACGC 60.807 66.667 0.00 0.00 0.00 5.34
242 245 2.807045 GCGAGAGGCACAGTCACG 60.807 66.667 0.00 0.00 42.87 4.35
256 259 1.602668 GGCACAAATTTGCTTCTGCGA 60.603 47.619 18.12 0.00 42.56 5.10
260 263 2.036346 GTGGAGGCACAAATTTGCTTCT 59.964 45.455 18.12 11.95 45.49 2.85
270 273 1.334160 TACTTCTCGTGGAGGCACAA 58.666 50.000 0.00 0.00 0.00 3.33
281 284 3.589988 AGAGGCATGTGTTTACTTCTCG 58.410 45.455 0.00 0.00 0.00 4.04
282 285 3.614616 CGAGAGGCATGTGTTTACTTCTC 59.385 47.826 0.00 0.00 0.00 2.87
287 290 2.668457 CTCACGAGAGGCATGTGTTTAC 59.332 50.000 1.41 0.00 38.26 2.01
289 292 1.344438 TCTCACGAGAGGCATGTGTTT 59.656 47.619 10.08 0.00 42.34 2.83
293 296 2.839486 TTTTCTCACGAGAGGCATGT 57.161 45.000 10.08 0.00 42.34 3.21
319 322 6.315393 GTGCCTCTCAGAAACGGAAAATAATA 59.685 38.462 0.00 0.00 0.00 0.98
328 331 1.009389 GTCGTGCCTCTCAGAAACGG 61.009 60.000 4.80 0.00 35.08 4.44
335 338 2.265739 GCATGGTCGTGCCTCTCA 59.734 61.111 3.93 0.00 39.18 3.27
358 361 0.242017 AGGCACGAATTTGCTTCAGC 59.758 50.000 2.32 0.00 42.56 4.26
359 362 2.253392 GAGGCACGAATTTGCTTCAG 57.747 50.000 8.83 0.00 45.50 3.02
364 367 1.226128 GCGAGAGGCACGAATTTGC 60.226 57.895 0.00 0.00 42.87 3.68
384 387 1.723220 GAGAGGTACGGGTTTGCTTC 58.277 55.000 0.00 0.00 0.00 3.86
435 439 0.317519 GACCGTGCCTTTTGGAAACG 60.318 55.000 0.00 0.00 45.10 3.60
436 440 0.317519 CGACCGTGCCTTTTGGAAAC 60.318 55.000 0.00 0.00 44.07 2.78
437 441 0.748729 ACGACCGTGCCTTTTGGAAA 60.749 50.000 0.00 0.00 44.07 3.13
440 444 2.637025 CACGACCGTGCCTTTTGG 59.363 61.111 9.69 0.00 39.39 3.28
461 466 0.179111 TACGGATTTGCCTCTGCGAG 60.179 55.000 0.00 0.00 41.78 5.03
465 470 3.068732 TGAGAGATACGGATTTGCCTCTG 59.931 47.826 1.45 0.00 31.86 3.35
466 471 3.068873 GTGAGAGATACGGATTTGCCTCT 59.931 47.826 0.00 0.00 34.11 3.69
469 474 2.128035 CGTGAGAGATACGGATTTGCC 58.872 52.381 0.00 0.00 37.86 4.52
499 504 7.279758 TCCTGAAAAACGAGAAAAATGCATTTT 59.720 29.630 27.73 27.73 43.85 1.82
500 505 6.760770 TCCTGAAAAACGAGAAAAATGCATTT 59.239 30.769 18.99 18.99 0.00 2.32
501 506 6.279882 TCCTGAAAAACGAGAAAAATGCATT 58.720 32.000 5.99 5.99 0.00 3.56
502 507 5.841810 TCCTGAAAAACGAGAAAAATGCAT 58.158 33.333 0.00 0.00 0.00 3.96
503 508 5.067153 TCTCCTGAAAAACGAGAAAAATGCA 59.933 36.000 0.00 0.00 29.82 3.96
504 509 5.399596 GTCTCCTGAAAAACGAGAAAAATGC 59.600 40.000 0.00 0.00 34.55 3.56
505 510 6.414987 GTGTCTCCTGAAAAACGAGAAAAATG 59.585 38.462 0.00 0.00 34.55 2.32
506 511 6.495706 GTGTCTCCTGAAAAACGAGAAAAAT 58.504 36.000 0.00 0.00 34.55 1.82
507 512 5.446741 CGTGTCTCCTGAAAAACGAGAAAAA 60.447 40.000 0.00 0.00 34.55 1.94
508 513 4.033587 CGTGTCTCCTGAAAAACGAGAAAA 59.966 41.667 0.00 0.00 34.55 2.29
509 514 3.554324 CGTGTCTCCTGAAAAACGAGAAA 59.446 43.478 0.00 0.00 34.55 2.52
510 515 3.120792 CGTGTCTCCTGAAAAACGAGAA 58.879 45.455 0.00 0.00 34.55 2.87
511 516 2.545113 CCGTGTCTCCTGAAAAACGAGA 60.545 50.000 0.00 0.00 31.58 4.04
512 517 1.792949 CCGTGTCTCCTGAAAAACGAG 59.207 52.381 0.00 0.00 31.58 4.18
513 518 1.860676 CCGTGTCTCCTGAAAAACGA 58.139 50.000 0.00 0.00 31.58 3.85
514 519 0.234884 GCCGTGTCTCCTGAAAAACG 59.765 55.000 0.00 0.00 0.00 3.60
515 520 0.591659 GGCCGTGTCTCCTGAAAAAC 59.408 55.000 0.00 0.00 0.00 2.43
554 564 7.706607 CCTCTCGGAGAAAAATGTTTTCTTTTT 59.293 33.333 15.19 0.00 38.73 1.94
561 571 3.253432 GTGCCTCTCGGAGAAAAATGTTT 59.747 43.478 9.32 0.00 34.09 2.83
563 573 2.427506 GTGCCTCTCGGAGAAAAATGT 58.572 47.619 9.32 0.00 34.09 2.71
564 574 1.394917 CGTGCCTCTCGGAGAAAAATG 59.605 52.381 9.32 0.00 34.09 2.32
565 575 1.726853 CGTGCCTCTCGGAGAAAAAT 58.273 50.000 9.32 0.00 34.09 1.82
598 618 1.018148 TCTTTCGCGAAAGGCACAAA 58.982 45.000 44.08 29.54 45.80 2.83
599 619 1.018148 TTCTTTCGCGAAAGGCACAA 58.982 45.000 44.08 33.23 45.80 3.33
600 620 1.234821 ATTCTTTCGCGAAAGGCACA 58.765 45.000 44.08 30.45 45.80 4.57
680 709 1.899814 AGAAACATGGTCGTGCCTCTA 59.100 47.619 0.00 0.00 38.35 2.43
681 710 0.687354 AGAAACATGGTCGTGCCTCT 59.313 50.000 0.00 0.00 38.35 3.69
682 711 1.079503 GAGAAACATGGTCGTGCCTC 58.920 55.000 0.00 0.00 38.35 4.70
683 712 0.670546 CGAGAAACATGGTCGTGCCT 60.671 55.000 0.00 0.00 38.35 4.75
684 713 1.787847 CGAGAAACATGGTCGTGCC 59.212 57.895 0.00 0.00 37.90 5.01
685 714 1.132640 GCGAGAAACATGGTCGTGC 59.867 57.895 0.00 0.41 36.09 5.34
686 715 1.416049 CGCGAGAAACATGGTCGTG 59.584 57.895 0.00 3.04 37.81 4.35
687 716 1.736645 CCGCGAGAAACATGGTCGT 60.737 57.895 8.23 0.00 36.09 4.34
688 717 1.011968 TTCCGCGAGAAACATGGTCG 61.012 55.000 8.23 1.08 36.77 4.79
689 718 0.721718 CTTCCGCGAGAAACATGGTC 59.278 55.000 8.23 0.00 32.88 4.02
690 719 0.034896 ACTTCCGCGAGAAACATGGT 59.965 50.000 8.23 0.58 32.88 3.55
691 720 2.004583 TACTTCCGCGAGAAACATGG 57.995 50.000 8.23 0.00 32.88 3.66
692 721 4.494199 GGATTTACTTCCGCGAGAAACATG 60.494 45.833 8.23 0.31 32.88 3.21
693 722 3.621715 GGATTTACTTCCGCGAGAAACAT 59.378 43.478 8.23 1.07 32.88 2.71
694 723 2.997986 GGATTTACTTCCGCGAGAAACA 59.002 45.455 8.23 0.00 32.88 2.83
697 734 3.536956 ATGGATTTACTTCCGCGAGAA 57.463 42.857 8.23 8.88 38.74 2.87
701 738 3.057734 GAGGTATGGATTTACTTCCGCG 58.942 50.000 0.00 0.00 38.74 6.46
709 746 6.207691 GCTTTTGCAAGAGGTATGGATTTA 57.792 37.500 17.82 0.00 46.58 1.40
799 837 3.878160 TTGGCTTTTGAACGGTCTTTT 57.122 38.095 0.33 0.00 0.00 2.27
827 865 9.868277 TTTTCAGCTTTTTAGATGTTTTTCTCA 57.132 25.926 0.00 0.00 0.00 3.27
867 905 7.923878 GCTCTGGGTGTTCACTTTAAATTTTAA 59.076 33.333 0.00 0.00 0.00 1.52
876 916 0.468226 TCGCTCTGGGTGTTCACTTT 59.532 50.000 2.98 0.00 0.00 2.66
880 920 1.069090 GTGTCGCTCTGGGTGTTCA 59.931 57.895 0.00 0.00 0.00 3.18
881 921 2.022129 CGTGTCGCTCTGGGTGTTC 61.022 63.158 0.00 0.00 0.00 3.18
883 923 3.224324 ACGTGTCGCTCTGGGTGT 61.224 61.111 0.00 0.00 0.00 4.16
887 927 2.801162 CGTCACGTGTCGCTCTGG 60.801 66.667 21.18 0.00 0.00 3.86
921 963 1.353103 CCTTAGAGCGCGCCATTTG 59.647 57.895 30.33 15.52 0.00 2.32
927 969 4.821589 ACTGGCCTTAGAGCGCGC 62.822 66.667 26.66 26.66 0.00 6.86
929 971 2.202946 GGACTGGCCTTAGAGCGC 60.203 66.667 3.32 0.00 0.00 5.92
939 981 0.890683 CAAGGGTCATTTGGACTGGC 59.109 55.000 0.00 0.00 46.16 4.85
976 1018 3.935828 GGTCAGACAGAAATGTAAGGAGC 59.064 47.826 2.17 0.00 0.00 4.70
977 1019 4.082190 TCGGTCAGACAGAAATGTAAGGAG 60.082 45.833 0.20 0.00 0.00 3.69
978 1020 3.830178 TCGGTCAGACAGAAATGTAAGGA 59.170 43.478 0.20 0.00 0.00 3.36
979 1021 4.188247 TCGGTCAGACAGAAATGTAAGG 57.812 45.455 0.20 0.00 0.00 2.69
980 1022 6.330278 TGTATCGGTCAGACAGAAATGTAAG 58.670 40.000 7.53 0.00 0.00 2.34
983 1025 4.801330 TGTATCGGTCAGACAGAAATGT 57.199 40.909 7.53 0.00 0.00 2.71
984 1026 6.668541 ATTTGTATCGGTCAGACAGAAATG 57.331 37.500 7.53 0.00 0.00 2.32
985 1027 6.910536 GATTTGTATCGGTCAGACAGAAAT 57.089 37.500 7.53 3.10 0.00 2.17
1008 1050 2.993471 GCCCATTGTGAAGGTGCCG 61.993 63.158 0.00 0.00 0.00 5.69
1009 1051 1.598701 GAGCCCATTGTGAAGGTGCC 61.599 60.000 0.00 0.00 0.00 5.01
1010 1052 0.895100 TGAGCCCATTGTGAAGGTGC 60.895 55.000 0.00 0.00 0.00 5.01
1011 1053 1.171308 CTGAGCCCATTGTGAAGGTG 58.829 55.000 0.00 0.00 0.00 4.00
1365 1572 2.737376 GAGGCGACGTTGGTCCAC 60.737 66.667 4.64 0.00 40.17 4.02
1471 1678 4.804139 CGAGAGTGCGGTAACAAGAATTAT 59.196 41.667 0.00 0.00 0.00 1.28
1489 1696 0.312416 GACCGATCCATCCACGAGAG 59.688 60.000 0.00 0.00 0.00 3.20
1493 1709 1.068083 CCAGACCGATCCATCCACG 59.932 63.158 0.00 0.00 0.00 4.94
1494 1710 0.105039 GTCCAGACCGATCCATCCAC 59.895 60.000 0.00 0.00 0.00 4.02
1541 1757 0.968901 ATGTGGGCAACTGCATCCTG 60.969 55.000 3.76 0.00 44.36 3.86
1543 1759 0.682209 AGATGTGGGCAACTGCATCC 60.682 55.000 3.76 0.00 43.54 3.51
1576 1793 6.885952 TTCGACAATTTCCTGGAATTAACA 57.114 33.333 10.45 0.00 0.00 2.41
1666 1883 0.957395 CAGCAGCACCAATTCCGAGT 60.957 55.000 0.00 0.00 0.00 4.18
1918 2138 7.010460 GCCATTTATTCACTCTATTTGGTTTGC 59.990 37.037 0.00 0.00 0.00 3.68
2107 2331 6.894339 ACATTTGGTTCTTTTACCTGTAGG 57.106 37.500 0.00 0.00 39.04 3.18
2212 2437 5.576447 ATGGAACGAAAACAGACAACTTT 57.424 34.783 0.00 0.00 0.00 2.66
2213 2438 5.576447 AATGGAACGAAAACAGACAACTT 57.424 34.783 0.00 0.00 0.00 2.66
2238 2463 2.625790 TGGTGCAAAAACATAGGTGGAC 59.374 45.455 0.00 0.00 0.00 4.02
2299 2524 3.988976 AATAGCAAGAGTGGAGAAGCA 57.011 42.857 0.00 0.00 0.00 3.91
2397 2622 1.006337 GATCCGAGGCAGCAGCTAG 60.006 63.158 0.00 0.00 41.70 3.42
2441 2666 1.002134 CTGCGGGTCAGGAATTGGT 60.002 57.895 0.00 0.00 39.15 3.67
2456 2681 5.246307 AGTGAAGATACAAAGGTTACCTGC 58.754 41.667 3.99 0.00 32.13 4.85
2635 2860 4.335416 CCACATTTGGTACAGGATGTTCT 58.665 43.478 0.00 0.00 42.62 3.01
2655 2880 1.610363 TGCCAGTTAAACGAATGCCA 58.390 45.000 0.00 0.00 0.00 4.92
2659 2884 3.192633 GGGACATTGCCAGTTAAACGAAT 59.807 43.478 0.00 0.00 0.00 3.34
2661 2886 2.156098 GGGACATTGCCAGTTAAACGA 58.844 47.619 0.00 0.00 0.00 3.85
2667 2892 3.033184 CCATATTGGGACATTGCCAGTT 58.967 45.455 0.00 0.00 39.66 3.16
2759 2984 1.142870 ACAGCAACAAGACCTGCCTTA 59.857 47.619 0.00 0.00 39.47 2.69
2763 2988 0.590195 CTCACAGCAACAAGACCTGC 59.410 55.000 0.00 0.00 38.91 4.85
2776 3001 4.208047 CACTCAAAACGAAGAGACTCACAG 59.792 45.833 5.02 0.00 35.83 3.66
2777 3002 4.112634 CACTCAAAACGAAGAGACTCACA 58.887 43.478 5.02 0.00 35.83 3.58
2799 3026 5.704217 ACTCGAAAGATGAACGCTAAATC 57.296 39.130 0.00 0.00 40.84 2.17
2999 3236 5.057843 ACAATTGCACTCCCATCATAGAT 57.942 39.130 5.05 0.00 0.00 1.98
3144 3381 8.016301 TGAAAGATGCTCATAAGAGTGTATCT 57.984 34.615 0.00 2.20 44.00 1.98
3145 3382 8.654230 TTGAAAGATGCTCATAAGAGTGTATC 57.346 34.615 0.00 0.11 44.00 2.24
3146 3383 9.107177 CTTTGAAAGATGCTCATAAGAGTGTAT 57.893 33.333 0.00 0.00 44.00 2.29
3147 3384 7.550551 CCTTTGAAAGATGCTCATAAGAGTGTA 59.449 37.037 6.49 0.00 44.00 2.90
3148 3385 6.373774 CCTTTGAAAGATGCTCATAAGAGTGT 59.626 38.462 6.49 0.00 44.00 3.55
3149 3386 6.677431 GCCTTTGAAAGATGCTCATAAGAGTG 60.677 42.308 6.49 0.00 44.00 3.51
3150 3387 5.356470 GCCTTTGAAAGATGCTCATAAGAGT 59.644 40.000 6.49 0.00 44.00 3.24
3151 3388 5.589452 AGCCTTTGAAAGATGCTCATAAGAG 59.411 40.000 6.49 0.00 44.96 2.85
3207 3448 6.295688 CGGTATATGCTAACTGTAGGGGAATT 60.296 42.308 0.00 0.00 0.00 2.17
3423 3667 2.086869 CTGGACAATAGTGCACAAGGG 58.913 52.381 21.04 8.30 41.46 3.95
3455 3699 2.756840 TGAGGTTCTGATGACAGCTG 57.243 50.000 13.48 13.48 43.17 4.24
3587 3831 4.676924 GGACAAAAAGCTCAACATCTTTCG 59.323 41.667 0.00 0.00 31.91 3.46
3604 3848 4.624913 AGAGGAGAGGTATGATGGACAAA 58.375 43.478 0.00 0.00 0.00 2.83
3610 3854 4.739793 AGAGGAAGAGGAGAGGTATGATG 58.260 47.826 0.00 0.00 0.00 3.07
3614 3858 3.797269 AGGAAGAGGAAGAGGAGAGGTAT 59.203 47.826 0.00 0.00 0.00 2.73
3650 3894 2.740981 CAAGAAGCTCAGCATCTTTCGT 59.259 45.455 14.51 0.00 42.67 3.85
3698 4027 3.195610 AGCACGTTCCTATGATTGACAGA 59.804 43.478 0.00 0.00 0.00 3.41
3701 4030 4.184629 AGAAGCACGTTCCTATGATTGAC 58.815 43.478 0.00 0.00 35.51 3.18
3818 4157 2.179427 CTCATATGGGATGGCTACCGA 58.821 52.381 0.00 0.00 0.00 4.69
3862 4201 3.331889 AGTTCCTCAACATTCCCATCAGT 59.668 43.478 0.00 0.00 34.60 3.41
3863 4202 3.960571 AGTTCCTCAACATTCCCATCAG 58.039 45.455 0.00 0.00 34.60 2.90
3908 4250 9.398538 ACAAACTAACCATACTGTGTTTCTTTA 57.601 29.630 0.00 0.00 0.00 1.85
3936 4278 6.016610 TGTTTAACCTTCTCTAACATGCCAAC 60.017 38.462 0.00 0.00 0.00 3.77
3953 4295 3.488553 GCTCACACACCACTTGTTTAACC 60.489 47.826 0.00 0.00 35.67 2.85


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

AutoCloner maintained by Alex Coulton.