Multiple sequence alignment - TraesCS7A01G086000

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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 TraesCS7A01G086000 chr7A 100.000 3820 0 0 1 3820 50135074 50138893 0.000000e+00 7055.0
1 TraesCS7A01G086000 chr7A 82.479 1210 185 14 1633 2819 49994046 49995251 0.000000e+00 1035.0
2 TraesCS7A01G086000 chr7A 86.289 547 62 7 951 1489 49993313 49993854 1.980000e-162 582.0
3 TraesCS7A01G086000 chr7A 79.231 260 49 5 1 258 34099552 34099808 3.920000e-40 176.0
4 TraesCS7A01G086000 chr4A 91.929 2577 150 22 946 3494 662566342 662568888 0.000000e+00 3554.0
5 TraesCS7A01G086000 chr4A 86.466 532 55 6 965 1489 662231759 662232280 5.540000e-158 568.0
6 TraesCS7A01G086000 chr4A 94.863 292 15 0 549 840 662566050 662566341 1.250000e-124 457.0
7 TraesCS7A01G086000 chr4A 90.303 330 24 4 3489 3813 662589213 662589539 3.530000e-115 425.0
8 TraesCS7A01G086000 chr4A 87.599 379 25 9 186 554 662565652 662566018 1.640000e-113 420.0
9 TraesCS7A01G086000 chr4A 82.418 455 71 6 1040 1488 621806464 621806013 4.630000e-104 388.0
10 TraesCS7A01G086000 chrUn 92.003 2301 139 21 1540 3820 264862735 264860460 0.000000e+00 3188.0
11 TraesCS7A01G086000 chrUn 92.037 2298 138 21 1540 3817 299069070 299071342 0.000000e+00 3188.0
12 TraesCS7A01G086000 chrUn 94.495 545 30 0 946 1490 264863278 264862734 0.000000e+00 841.0
13 TraesCS7A01G086000 chrUn 94.495 545 30 0 946 1490 299068527 299069071 0.000000e+00 841.0
14 TraesCS7A01G086000 chrUn 85.792 549 37 22 7 554 264866449 264865941 9.330000e-151 544.0
15 TraesCS7A01G086000 chrUn 85.586 555 39 22 1 554 280426467 280426981 9.330000e-151 544.0
16 TraesCS7A01G086000 chrUn 85.586 555 39 22 1 554 280433480 280433994 9.330000e-151 544.0
17 TraesCS7A01G086000 chrUn 85.792 549 37 22 7 554 305064869 305064361 9.330000e-151 544.0
18 TraesCS7A01G086000 chrUn 95.149 268 12 1 573 840 264863545 264863279 4.560000e-114 422.0
19 TraesCS7A01G086000 chrUn 95.149 268 12 1 573 840 299068260 299068526 4.560000e-114 422.0
20 TraesCS7A01G086000 chrUn 82.292 480 74 6 1016 1488 306906396 306905921 4.600000e-109 405.0
21 TraesCS7A01G086000 chr7D 94.977 1951 88 3 946 2888 47481679 47483627 0.000000e+00 3051.0
22 TraesCS7A01G086000 chr7D 95.866 895 31 6 2926 3817 47483622 47484513 0.000000e+00 1443.0
23 TraesCS7A01G086000 chr7D 83.045 1215 181 13 1627 2819 47449528 47448317 0.000000e+00 1079.0
24 TraesCS7A01G086000 chr7D 87.242 533 55 7 965 1489 47450234 47449707 2.540000e-166 595.0
25 TraesCS7A01G086000 chr7D 87.129 303 11 6 549 840 47481393 47481678 6.160000e-83 318.0
26 TraesCS7A01G086000 chr7D 92.760 221 10 3 335 555 47481148 47481362 7.970000e-82 315.0
27 TraesCS7A01G086000 chr7D 90.196 153 15 0 186 338 47480837 47480989 2.330000e-47 200.0
28 TraesCS7A01G086000 chr7D 80.385 260 48 3 1 258 634289671 634289929 1.080000e-45 195.0
29 TraesCS7A01G086000 chr5B 82.637 455 70 6 1040 1488 690102710 690103161 9.950000e-106 394.0
30 TraesCS7A01G086000 chr5B 76.434 488 105 8 1635 2120 712009094 712008615 4.900000e-64 255.0
31 TraesCS7A01G086000 chr5B 76.434 488 105 8 1635 2120 712026546 712026067 4.900000e-64 255.0
32 TraesCS7A01G086000 chr5A 92.793 111 7 1 839 949 402547779 402547888 3.950000e-35 159.0
33 TraesCS7A01G086000 chr1D 77.953 254 55 1 6 258 456174134 456174387 1.420000e-34 158.0
34 TraesCS7A01G086000 chr1A 79.535 215 32 5 18 222 449845654 449845442 3.980000e-30 143.0
35 TraesCS7A01G086000 chr7B 89.189 111 11 1 837 947 592559007 592558898 1.850000e-28 137.0
36 TraesCS7A01G086000 chr2D 80.864 162 28 2 39 199 567002299 567002140 1.440000e-24 124.0
37 TraesCS7A01G086000 chr2D 95.455 44 0 2 832 873 119669669 119669626 6.850000e-08 69.4


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 TraesCS7A01G086000 chr7A 50135074 50138893 3819 False 7055.000000 7055 100.000000 1 3820 1 chr7A.!!$F2 3819
1 TraesCS7A01G086000 chr7A 49993313 49995251 1938 False 808.500000 1035 84.384000 951 2819 2 chr7A.!!$F3 1868
2 TraesCS7A01G086000 chr4A 662565652 662568888 3236 False 1477.000000 3554 91.463667 186 3494 3 chr4A.!!$F3 3308
3 TraesCS7A01G086000 chr4A 662231759 662232280 521 False 568.000000 568 86.466000 965 1489 1 chr4A.!!$F1 524
4 TraesCS7A01G086000 chrUn 299068260 299071342 3082 False 1483.666667 3188 93.893667 573 3817 3 chrUn.!!$F3 3244
5 TraesCS7A01G086000 chrUn 264860460 264866449 5989 True 1248.750000 3188 91.859750 7 3820 4 chrUn.!!$R3 3813
6 TraesCS7A01G086000 chrUn 280426467 280426981 514 False 544.000000 544 85.586000 1 554 1 chrUn.!!$F1 553
7 TraesCS7A01G086000 chrUn 280433480 280433994 514 False 544.000000 544 85.586000 1 554 1 chrUn.!!$F2 553
8 TraesCS7A01G086000 chrUn 305064361 305064869 508 True 544.000000 544 85.792000 7 554 1 chrUn.!!$R1 547
9 TraesCS7A01G086000 chr7D 47480837 47484513 3676 False 1065.400000 3051 92.185600 186 3817 5 chr7D.!!$F2 3631
10 TraesCS7A01G086000 chr7D 47448317 47450234 1917 True 837.000000 1079 85.143500 965 2819 2 chr7D.!!$R1 1854

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
66 67 0.108329 GATCGAAGCCCGGAAGACAA 60.108 55.000 0.73 0.0 39.14 3.18 F
67 68 0.323629 ATCGAAGCCCGGAAGACAAA 59.676 50.000 0.73 0.0 39.14 2.83 F
68 69 0.601841 TCGAAGCCCGGAAGACAAAC 60.602 55.000 0.73 0.0 39.14 2.93 F
258 259 0.820871 AGAGAGAGTTTGCCCTAGCG 59.179 55.000 0.00 0.0 44.31 4.26 F
2057 4781 1.070134 CCTCTGGAAGAAACCACGTGA 59.930 52.381 19.30 0.0 46.34 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 4693 0.911769 TTAGGGTCCAGGTGATGCTG 59.088 55.000 0.00 0.00 0.00 4.41 R
2013 4737 1.627864 TGAGGACGTCAATGAGGTCA 58.372 50.000 29.42 13.34 45.59 4.02 R
2057 4781 3.821033 GTCCTTGGTGAAGCTAAATGTGT 59.179 43.478 0.00 0.00 0.00 3.72 R
2187 4936 0.239082 ACGAACGTCGACTGCACATA 59.761 50.000 14.70 0.00 43.74 2.29 R
3648 6408 1.080569 GTGATTTGCAAGGCCCACG 60.081 57.895 0.00 0.00 0.00 4.94 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
17 18 4.492160 TACGCCGGAGCTTCGCTG 62.492 66.667 9.56 5.66 39.88 5.18
65 66 1.515954 GATCGAAGCCCGGAAGACA 59.484 57.895 0.73 0.00 39.14 3.41
66 67 0.108329 GATCGAAGCCCGGAAGACAA 60.108 55.000 0.73 0.00 39.14 3.18
67 68 0.323629 ATCGAAGCCCGGAAGACAAA 59.676 50.000 0.73 0.00 39.14 2.83
68 69 0.601841 TCGAAGCCCGGAAGACAAAC 60.602 55.000 0.73 0.00 39.14 2.93
161 162 3.673597 AGAGAGGAGGCACCCGGA 61.674 66.667 0.73 0.00 40.05 5.14
164 165 1.457831 AGAGGAGGCACCCGGATAC 60.458 63.158 0.73 0.00 40.05 2.24
171 172 2.070650 GCACCCGGATACCCCTTCT 61.071 63.158 0.73 0.00 0.00 2.85
177 178 1.532238 GGATACCCCTTCTGGCCAC 59.468 63.158 0.00 0.00 0.00 5.01
258 259 0.820871 AGAGAGAGTTTGCCCTAGCG 59.179 55.000 0.00 0.00 44.31 4.26
274 282 3.083997 CGACTGAGGGGAAGGGGG 61.084 72.222 0.00 0.00 0.00 5.40
322 330 2.798148 AATGAAGGTGGCCGGTCGAC 62.798 60.000 7.13 7.13 0.00 4.20
374 544 3.934579 CACAACACATACATGAGCTAGCA 59.065 43.478 18.83 0.00 0.00 3.49
386 556 4.640789 TGAGCTAGCAGAAGTAGTTAGC 57.359 45.455 18.83 0.00 43.46 3.09
405 575 4.346734 AGCTCATTTGCTAATTCACACG 57.653 40.909 0.00 0.00 42.10 4.49
444 614 4.680237 TTGTGAGGGGCGCTCGTG 62.680 66.667 24.17 0.00 0.00 4.35
480 650 1.284715 CCGCCCAAAGTTCGTTTCC 59.715 57.895 0.00 0.00 0.00 3.13
521 693 6.165700 ACTTTCAAACAGCAAAATGGATCT 57.834 33.333 0.00 0.00 0.00 2.75
522 694 7.288810 ACTTTCAAACAGCAAAATGGATCTA 57.711 32.000 0.00 0.00 0.00 1.98
523 695 7.725251 ACTTTCAAACAGCAAAATGGATCTAA 58.275 30.769 0.00 0.00 0.00 2.10
524 696 8.203485 ACTTTCAAACAGCAAAATGGATCTAAA 58.797 29.630 0.00 0.00 0.00 1.85
525 697 8.592105 TTTCAAACAGCAAAATGGATCTAAAG 57.408 30.769 0.00 0.00 0.00 1.85
561 774 4.808364 GCAGAGGAGACAAATCAGACATAC 59.192 45.833 0.00 0.00 0.00 2.39
651 3204 2.983433 CTGACTTCGCAGCCATAGG 58.017 57.895 0.00 0.00 0.00 2.57
763 3320 9.035890 TCTTCTCCTTCAAATACTCATCAACTA 57.964 33.333 0.00 0.00 0.00 2.24
840 3404 4.423732 CCTTTGCACAGCATATTTGGTAC 58.576 43.478 0.00 0.00 38.76 3.34
841 3405 4.158394 CCTTTGCACAGCATATTTGGTACT 59.842 41.667 0.00 0.00 38.76 2.73
842 3406 5.336690 CCTTTGCACAGCATATTTGGTACTT 60.337 40.000 0.00 0.00 38.76 2.24
843 3407 4.963276 TGCACAGCATATTTGGTACTTC 57.037 40.909 0.00 0.00 31.71 3.01
844 3408 3.694072 TGCACAGCATATTTGGTACTTCC 59.306 43.478 0.00 0.00 31.71 3.46
845 3409 3.947834 GCACAGCATATTTGGTACTTCCT 59.052 43.478 0.00 0.00 37.07 3.36
846 3410 4.035675 GCACAGCATATTTGGTACTTCCTC 59.964 45.833 0.00 0.00 37.07 3.71
847 3411 5.431765 CACAGCATATTTGGTACTTCCTCT 58.568 41.667 0.00 0.00 37.07 3.69
848 3412 5.295292 CACAGCATATTTGGTACTTCCTCTG 59.705 44.000 0.00 0.00 37.07 3.35
849 3413 5.045578 ACAGCATATTTGGTACTTCCTCTGT 60.046 40.000 0.00 0.00 37.07 3.41
850 3414 5.882557 CAGCATATTTGGTACTTCCTCTGTT 59.117 40.000 0.00 0.00 37.07 3.16
851 3415 6.037610 CAGCATATTTGGTACTTCCTCTGTTC 59.962 42.308 0.00 0.00 37.07 3.18
852 3416 5.880332 GCATATTTGGTACTTCCTCTGTTCA 59.120 40.000 0.00 0.00 37.07 3.18
853 3417 6.543831 GCATATTTGGTACTTCCTCTGTTCAT 59.456 38.462 0.00 0.00 37.07 2.57
854 3418 7.067494 GCATATTTGGTACTTCCTCTGTTCATT 59.933 37.037 0.00 0.00 37.07 2.57
855 3419 8.960591 CATATTTGGTACTTCCTCTGTTCATTT 58.039 33.333 0.00 0.00 37.07 2.32
856 3420 7.839680 ATTTGGTACTTCCTCTGTTCATTTT 57.160 32.000 0.00 0.00 37.07 1.82
857 3421 7.654022 TTTGGTACTTCCTCTGTTCATTTTT 57.346 32.000 0.00 0.00 37.07 1.94
858 3422 8.754991 TTTGGTACTTCCTCTGTTCATTTTTA 57.245 30.769 0.00 0.00 37.07 1.52
859 3423 8.934023 TTGGTACTTCCTCTGTTCATTTTTAT 57.066 30.769 0.00 0.00 37.07 1.40
887 3451 7.602517 ACATTTTAGACTATTCAGACAGTGC 57.397 36.000 0.00 0.00 0.00 4.40
888 3452 6.595716 ACATTTTAGACTATTCAGACAGTGCC 59.404 38.462 0.00 0.00 0.00 5.01
889 3453 4.737855 TTAGACTATTCAGACAGTGCCC 57.262 45.455 0.00 0.00 0.00 5.36
890 3454 2.540383 AGACTATTCAGACAGTGCCCA 58.460 47.619 0.00 0.00 0.00 5.36
891 3455 2.906389 AGACTATTCAGACAGTGCCCAA 59.094 45.455 0.00 0.00 0.00 4.12
892 3456 3.327757 AGACTATTCAGACAGTGCCCAAA 59.672 43.478 0.00 0.00 0.00 3.28
893 3457 4.072131 GACTATTCAGACAGTGCCCAAAA 58.928 43.478 0.00 0.00 0.00 2.44
894 3458 3.821033 ACTATTCAGACAGTGCCCAAAAC 59.179 43.478 0.00 0.00 0.00 2.43
895 3459 2.136298 TTCAGACAGTGCCCAAAACA 57.864 45.000 0.00 0.00 0.00 2.83
896 3460 2.136298 TCAGACAGTGCCCAAAACAA 57.864 45.000 0.00 0.00 0.00 2.83
897 3461 2.665165 TCAGACAGTGCCCAAAACAAT 58.335 42.857 0.00 0.00 0.00 2.71
898 3462 3.030291 TCAGACAGTGCCCAAAACAATT 58.970 40.909 0.00 0.00 0.00 2.32
899 3463 3.068024 TCAGACAGTGCCCAAAACAATTC 59.932 43.478 0.00 0.00 0.00 2.17
900 3464 3.030291 AGACAGTGCCCAAAACAATTCA 58.970 40.909 0.00 0.00 0.00 2.57
901 3465 3.450457 AGACAGTGCCCAAAACAATTCAA 59.550 39.130 0.00 0.00 0.00 2.69
902 3466 4.081198 AGACAGTGCCCAAAACAATTCAAA 60.081 37.500 0.00 0.00 0.00 2.69
903 3467 4.583871 ACAGTGCCCAAAACAATTCAAAA 58.416 34.783 0.00 0.00 0.00 2.44
904 3468 4.394610 ACAGTGCCCAAAACAATTCAAAAC 59.605 37.500 0.00 0.00 0.00 2.43
905 3469 4.635324 CAGTGCCCAAAACAATTCAAAACT 59.365 37.500 0.00 0.00 0.00 2.66
906 3470 5.814705 CAGTGCCCAAAACAATTCAAAACTA 59.185 36.000 0.00 0.00 0.00 2.24
907 3471 6.018832 CAGTGCCCAAAACAATTCAAAACTAG 60.019 38.462 0.00 0.00 0.00 2.57
908 3472 5.815222 GTGCCCAAAACAATTCAAAACTAGT 59.185 36.000 0.00 0.00 0.00 2.57
909 3473 6.315144 GTGCCCAAAACAATTCAAAACTAGTT 59.685 34.615 1.12 1.12 0.00 2.24
910 3474 6.314896 TGCCCAAAACAATTCAAAACTAGTTG 59.685 34.615 9.34 0.00 0.00 3.16
911 3475 6.315144 GCCCAAAACAATTCAAAACTAGTTGT 59.685 34.615 9.34 0.00 34.74 3.32
912 3476 7.465379 GCCCAAAACAATTCAAAACTAGTTGTC 60.465 37.037 9.34 0.00 32.32 3.18
913 3477 7.763985 CCCAAAACAATTCAAAACTAGTTGTCT 59.236 33.333 9.34 0.00 32.32 3.41
914 3478 9.796120 CCAAAACAATTCAAAACTAGTTGTCTA 57.204 29.630 9.34 0.00 32.32 2.59
919 3483 9.498307 ACAATTCAAAACTAGTTGTCTAAAACG 57.502 29.630 9.34 0.00 35.13 3.60
920 3484 9.498307 CAATTCAAAACTAGTTGTCTAAAACGT 57.502 29.630 9.34 0.00 35.13 3.99
921 3485 9.712359 AATTCAAAACTAGTTGTCTAAAACGTC 57.288 29.630 9.34 0.00 35.13 4.34
922 3486 7.237920 TCAAAACTAGTTGTCTAAAACGTCC 57.762 36.000 9.34 0.00 35.13 4.79
923 3487 7.043565 TCAAAACTAGTTGTCTAAAACGTCCT 58.956 34.615 9.34 0.00 35.13 3.85
924 3488 8.196771 TCAAAACTAGTTGTCTAAAACGTCCTA 58.803 33.333 9.34 0.00 35.13 2.94
925 3489 8.985805 CAAAACTAGTTGTCTAAAACGTCCTAT 58.014 33.333 9.34 0.00 35.13 2.57
963 3527 2.397549 AGTAAAGTTCGCACGTACACC 58.602 47.619 2.72 0.00 0.00 4.16
1062 3632 2.826777 AATGGCAGCCCGTCCTCTTG 62.827 60.000 9.64 0.00 0.00 3.02
1365 3941 1.437986 GAAGCGGCTGACCTACGAT 59.562 57.895 1.81 0.00 0.00 3.73
1396 3972 4.728102 CGTTCGCACCCTACGGCA 62.728 66.667 0.00 0.00 0.00 5.69
1437 4013 1.080434 GCTTCTCACGGTCGAGCTT 60.080 57.895 13.48 0.00 32.75 3.74
1604 4221 1.291877 ATCGGCAGTCAAACGAGCAC 61.292 55.000 0.00 0.00 40.21 4.40
1791 4515 2.237143 TGGCAGTGATAAGTTCTCCCAG 59.763 50.000 0.00 0.00 0.00 4.45
1969 4693 2.948315 GCCTTCTTTGAGATGGTCATCC 59.052 50.000 7.28 1.07 40.56 3.51
2057 4781 1.070134 CCTCTGGAAGAAACCACGTGA 59.930 52.381 19.30 0.00 46.34 4.35
2448 5197 2.169144 ACCATGCGAGACATCAAGATCA 59.831 45.455 0.00 0.00 36.64 2.92
2512 5261 3.532155 GGCGATCGGCAGAGACCT 61.532 66.667 33.81 0.00 46.16 3.85
2672 5421 1.722011 CCACCATCGAGTTTACGCTT 58.278 50.000 0.00 0.00 0.00 4.68
2793 5542 1.136147 CCACTCGTACTCGTTCCCG 59.864 63.158 0.00 0.00 38.33 5.14
2882 5631 3.093057 ACATCCTGGACTAGTGTCTCAC 58.907 50.000 0.00 0.00 42.54 3.51
2946 5695 4.517832 GTGTAAAAGTGGGAGTAAAGTGGG 59.482 45.833 0.00 0.00 0.00 4.61
3012 5761 3.275617 ACTGCCGCCAAATCTACAATA 57.724 42.857 0.00 0.00 0.00 1.90
3359 6113 2.872408 GCACAGCCAGCATTTAGGA 58.128 52.632 0.00 0.00 0.00 2.94
3384 6138 3.895704 AAAAAGGGCACTAGGGAGAAA 57.104 42.857 0.00 0.00 0.00 2.52
3394 6148 4.097286 GCACTAGGGAGAAAGACTGTCTAG 59.903 50.000 11.30 4.67 35.69 2.43
3397 6151 3.511477 AGGGAGAAAGACTGTCTAGCAA 58.489 45.455 11.30 0.00 0.00 3.91
3398 6152 3.904339 AGGGAGAAAGACTGTCTAGCAAA 59.096 43.478 11.30 0.00 0.00 3.68
3424 6178 6.899393 AACCACACATATTGTTCTGTGAAT 57.101 33.333 9.46 0.00 44.35 2.57
3430 6184 6.347644 ACACATATTGTTCTGTGAATCACACG 60.348 38.462 12.63 8.97 43.59 4.49
3476 6230 3.736483 CAACAGAGCCGTTGTGCT 58.264 55.556 3.69 0.00 46.37 4.40
3481 6235 3.357079 GAGCCGTTGTGCTGGTGG 61.357 66.667 0.00 0.00 42.95 4.61
3486 6240 2.985847 GTTGTGCTGGTGGGAGGC 60.986 66.667 0.00 0.00 0.00 4.70
3515 6269 4.263068 CCAACTGAATCAACTAGTGGAGGT 60.263 45.833 6.07 0.00 0.00 3.85
3523 6279 1.178276 ACTAGTGGAGGTTGAGAGCG 58.822 55.000 0.00 0.00 0.00 5.03
3554 6310 8.299570 CCCAACTAATAATCAAGTAATGGATGC 58.700 37.037 0.00 0.00 28.86 3.91
3641 6401 1.251251 AGGTTTGCTCTCAATGTGGC 58.749 50.000 0.00 0.00 31.33 5.01
3648 6408 0.376152 CTCTCAATGTGGCGACATGC 59.624 55.000 15.55 0.00 42.30 4.06
3672 6432 2.027837 GGGCCTTGCAAATCACAGAAAT 60.028 45.455 0.84 0.00 0.00 2.17
3698 6458 3.693578 TCGAAGCATGGCAATGTCAATTA 59.306 39.130 2.31 0.00 36.08 1.40
3731 6491 6.976636 TTTGTGGCTTTGGTAAAAGAAAAG 57.023 33.333 2.46 0.00 44.81 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.736978 CTTCGATCCTCCACGAGATTG 58.263 52.381 0.00 0.00 39.59 2.67
65 66 2.357952 GGCGGTGTTTCTTCTTGAGTTT 59.642 45.455 0.00 0.00 0.00 2.66
66 67 1.947456 GGCGGTGTTTCTTCTTGAGTT 59.053 47.619 0.00 0.00 0.00 3.01
67 68 1.134220 TGGCGGTGTTTCTTCTTGAGT 60.134 47.619 0.00 0.00 0.00 3.41
68 69 1.593196 TGGCGGTGTTTCTTCTTGAG 58.407 50.000 0.00 0.00 0.00 3.02
124 125 6.966751 TCTCTGGCTAGTAGTTTAGGTTAGA 58.033 40.000 0.00 0.00 0.00 2.10
127 128 4.957327 CCTCTCTGGCTAGTAGTTTAGGTT 59.043 45.833 0.00 0.00 0.00 3.50
144 145 1.656092 TATCCGGGTGCCTCCTCTCT 61.656 60.000 0.00 0.00 36.25 3.10
161 162 2.375345 CGGTGGCCAGAAGGGGTAT 61.375 63.158 5.11 0.00 37.04 2.73
258 259 2.125225 ACCCCCTTCCCCTCAGTC 59.875 66.667 0.00 0.00 0.00 3.51
274 282 5.507985 CCTCACTCTTTTCCCAACATTTCAC 60.508 44.000 0.00 0.00 0.00 3.18
322 330 9.436957 GTTATATACCAAGTATGTTGGATGGAG 57.563 37.037 14.05 0.00 42.06 3.86
356 526 4.161189 ACTTCTGCTAGCTCATGTATGTGT 59.839 41.667 17.23 0.00 0.00 3.72
357 527 4.691175 ACTTCTGCTAGCTCATGTATGTG 58.309 43.478 17.23 0.00 0.00 3.21
358 528 5.596361 ACTACTTCTGCTAGCTCATGTATGT 59.404 40.000 17.23 10.73 0.00 2.29
359 529 6.083098 ACTACTTCTGCTAGCTCATGTATG 57.917 41.667 17.23 10.25 0.00 2.39
360 530 6.723298 AACTACTTCTGCTAGCTCATGTAT 57.277 37.500 17.23 0.00 0.00 2.29
386 556 5.536554 ACTCGTGTGAATTAGCAAATGAG 57.463 39.130 0.00 0.00 42.38 2.90
405 575 4.473477 ACCCACTAGCTCAACATAACTC 57.527 45.455 0.00 0.00 0.00 3.01
480 650 7.477144 TGAAAGTATCTGTGTACACTTTGTG 57.523 36.000 25.60 11.22 40.38 3.33
521 693 5.068591 TCCTCTGCGCATGATACTTACTTTA 59.931 40.000 12.24 0.00 0.00 1.85
522 694 4.122776 CCTCTGCGCATGATACTTACTTT 58.877 43.478 12.24 0.00 0.00 2.66
523 695 3.384789 TCCTCTGCGCATGATACTTACTT 59.615 43.478 12.24 0.00 0.00 2.24
524 696 2.959030 TCCTCTGCGCATGATACTTACT 59.041 45.455 12.24 0.00 0.00 2.24
525 697 3.004839 TCTCCTCTGCGCATGATACTTAC 59.995 47.826 12.24 0.00 0.00 2.34
651 3204 7.286313 AGTACTACTCTATGGTTGGTACTACC 58.714 42.308 0.00 9.83 36.64 3.18
763 3320 2.375174 TGTGGTCAGCTATCCCAAGTTT 59.625 45.455 0.12 0.00 0.00 2.66
861 3425 8.507249 GCACTGTCTGAATAGTCTAAAATGTTT 58.493 33.333 0.00 0.00 0.00 2.83
862 3426 7.119846 GGCACTGTCTGAATAGTCTAAAATGTT 59.880 37.037 0.00 0.00 0.00 2.71
863 3427 6.595716 GGCACTGTCTGAATAGTCTAAAATGT 59.404 38.462 0.00 0.00 0.00 2.71
864 3428 6.037610 GGGCACTGTCTGAATAGTCTAAAATG 59.962 42.308 0.00 0.00 0.00 2.32
865 3429 6.116126 GGGCACTGTCTGAATAGTCTAAAAT 58.884 40.000 0.00 0.00 0.00 1.82
866 3430 5.012664 TGGGCACTGTCTGAATAGTCTAAAA 59.987 40.000 0.00 0.00 0.00 1.52
867 3431 4.530553 TGGGCACTGTCTGAATAGTCTAAA 59.469 41.667 0.00 0.00 0.00 1.85
868 3432 4.093743 TGGGCACTGTCTGAATAGTCTAA 58.906 43.478 0.00 0.00 0.00 2.10
869 3433 3.708451 TGGGCACTGTCTGAATAGTCTA 58.292 45.455 0.00 0.00 0.00 2.59
870 3434 2.540383 TGGGCACTGTCTGAATAGTCT 58.460 47.619 0.00 0.00 0.00 3.24
871 3435 3.334583 TTGGGCACTGTCTGAATAGTC 57.665 47.619 0.00 0.00 0.00 2.59
872 3436 3.788227 TTTGGGCACTGTCTGAATAGT 57.212 42.857 0.00 0.00 0.00 2.12
873 3437 3.820467 TGTTTTGGGCACTGTCTGAATAG 59.180 43.478 0.00 0.00 0.00 1.73
874 3438 3.826524 TGTTTTGGGCACTGTCTGAATA 58.173 40.909 0.00 0.00 0.00 1.75
875 3439 2.665165 TGTTTTGGGCACTGTCTGAAT 58.335 42.857 0.00 0.00 0.00 2.57
876 3440 2.136298 TGTTTTGGGCACTGTCTGAA 57.864 45.000 0.00 0.00 0.00 3.02
877 3441 2.136298 TTGTTTTGGGCACTGTCTGA 57.864 45.000 0.00 0.00 0.00 3.27
878 3442 3.181477 TGAATTGTTTTGGGCACTGTCTG 60.181 43.478 0.00 0.00 0.00 3.51
879 3443 3.030291 TGAATTGTTTTGGGCACTGTCT 58.970 40.909 0.00 0.00 0.00 3.41
880 3444 3.451141 TGAATTGTTTTGGGCACTGTC 57.549 42.857 0.00 0.00 0.00 3.51
881 3445 3.902881 TTGAATTGTTTTGGGCACTGT 57.097 38.095 0.00 0.00 0.00 3.55
882 3446 4.635324 AGTTTTGAATTGTTTTGGGCACTG 59.365 37.500 0.00 0.00 0.00 3.66
883 3447 4.842574 AGTTTTGAATTGTTTTGGGCACT 58.157 34.783 0.00 0.00 0.00 4.40
884 3448 5.815222 ACTAGTTTTGAATTGTTTTGGGCAC 59.185 36.000 0.00 0.00 0.00 5.01
885 3449 5.983540 ACTAGTTTTGAATTGTTTTGGGCA 58.016 33.333 0.00 0.00 0.00 5.36
886 3450 6.315144 ACAACTAGTTTTGAATTGTTTTGGGC 59.685 34.615 5.07 0.00 29.30 5.36
887 3451 7.763985 AGACAACTAGTTTTGAATTGTTTTGGG 59.236 33.333 5.07 0.00 33.76 4.12
888 3452 8.702163 AGACAACTAGTTTTGAATTGTTTTGG 57.298 30.769 5.07 0.00 33.76 3.28
893 3457 9.498307 CGTTTTAGACAACTAGTTTTGAATTGT 57.502 29.630 5.07 0.00 36.24 2.71
894 3458 9.498307 ACGTTTTAGACAACTAGTTTTGAATTG 57.502 29.630 5.07 0.00 0.00 2.32
895 3459 9.712359 GACGTTTTAGACAACTAGTTTTGAATT 57.288 29.630 5.07 0.00 0.00 2.17
896 3460 8.340443 GGACGTTTTAGACAACTAGTTTTGAAT 58.660 33.333 5.07 0.00 0.00 2.57
897 3461 7.550196 AGGACGTTTTAGACAACTAGTTTTGAA 59.450 33.333 5.07 0.00 0.00 2.69
898 3462 7.043565 AGGACGTTTTAGACAACTAGTTTTGA 58.956 34.615 5.07 0.00 0.00 2.69
899 3463 7.242914 AGGACGTTTTAGACAACTAGTTTTG 57.757 36.000 5.07 0.00 0.00 2.44
927 3491 3.473923 TTACTCCCTCCGTTCGTTTTT 57.526 42.857 0.00 0.00 0.00 1.94
928 3492 3.181462 ACTTTACTCCCTCCGTTCGTTTT 60.181 43.478 0.00 0.00 0.00 2.43
929 3493 2.366590 ACTTTACTCCCTCCGTTCGTTT 59.633 45.455 0.00 0.00 0.00 3.60
930 3494 1.966354 ACTTTACTCCCTCCGTTCGTT 59.034 47.619 0.00 0.00 0.00 3.85
931 3495 1.625511 ACTTTACTCCCTCCGTTCGT 58.374 50.000 0.00 0.00 0.00 3.85
932 3496 2.603953 GAACTTTACTCCCTCCGTTCG 58.396 52.381 0.00 0.00 0.00 3.95
933 3497 2.603953 CGAACTTTACTCCCTCCGTTC 58.396 52.381 0.00 0.00 0.00 3.95
934 3498 1.337541 GCGAACTTTACTCCCTCCGTT 60.338 52.381 0.00 0.00 0.00 4.44
935 3499 0.245813 GCGAACTTTACTCCCTCCGT 59.754 55.000 0.00 0.00 0.00 4.69
936 3500 0.245539 TGCGAACTTTACTCCCTCCG 59.754 55.000 0.00 0.00 0.00 4.63
937 3501 1.723220 GTGCGAACTTTACTCCCTCC 58.277 55.000 0.00 0.00 0.00 4.30
938 3502 1.336609 ACGTGCGAACTTTACTCCCTC 60.337 52.381 0.00 0.00 0.00 4.30
939 3503 0.677842 ACGTGCGAACTTTACTCCCT 59.322 50.000 0.00 0.00 0.00 4.20
940 3504 1.988467 GTACGTGCGAACTTTACTCCC 59.012 52.381 0.00 0.00 0.00 4.30
941 3505 2.406357 GTGTACGTGCGAACTTTACTCC 59.594 50.000 0.00 0.00 0.00 3.85
942 3506 2.406357 GGTGTACGTGCGAACTTTACTC 59.594 50.000 0.00 0.00 0.00 2.59
943 3507 2.223782 TGGTGTACGTGCGAACTTTACT 60.224 45.455 0.00 0.00 0.00 2.24
944 3508 2.126467 TGGTGTACGTGCGAACTTTAC 58.874 47.619 0.00 0.00 0.00 2.01
1062 3632 2.637947 GAAAGGATGGAGAGAAGTGCC 58.362 52.381 0.00 0.00 0.00 5.01
1396 3972 2.654877 CACCTTCCGCCAGTACGT 59.345 61.111 0.00 0.00 0.00 3.57
1408 3984 1.227943 TGAGAAGCTTGCGCACCTT 60.228 52.632 19.15 19.15 39.10 3.50
1428 4004 4.177229 GTGCTGAGAAGCTCGACC 57.823 61.111 0.00 0.00 32.35 4.79
1464 4040 1.739929 CTCATGGCGTGCGTACCAA 60.740 57.895 0.65 0.00 39.96 3.67
1604 4221 9.509855 CATTTAAGTAACTAGCTAGACAGACTG 57.490 37.037 27.45 0.00 0.00 3.51
1791 4515 2.227865 TGCGGCCTGAAAACTGTTATTC 59.772 45.455 0.00 1.52 0.00 1.75
1857 4581 3.787001 CCGGGGAGCAAGTCCTCC 61.787 72.222 0.00 0.00 44.30 4.30
1969 4693 0.911769 TTAGGGTCCAGGTGATGCTG 59.088 55.000 0.00 0.00 0.00 4.41
2013 4737 1.627864 TGAGGACGTCAATGAGGTCA 58.372 50.000 29.42 13.34 45.59 4.02
2057 4781 3.821033 GTCCTTGGTGAAGCTAAATGTGT 59.179 43.478 0.00 0.00 0.00 3.72
2187 4936 0.239082 ACGAACGTCGACTGCACATA 59.761 50.000 14.70 0.00 43.74 2.29
2577 5326 0.543277 TCTGGATGCTCGCCTTTGAT 59.457 50.000 0.00 0.00 0.00 2.57
2793 5542 3.192922 GTCGTGGTGGTATGCGGC 61.193 66.667 0.00 0.00 0.00 6.53
2982 5731 4.497473 TTTGGCGGCAGTAAATATATGC 57.503 40.909 12.87 0.00 39.25 3.14
3012 5761 7.769044 AGCGACAAAACAATATATCTAGGTGTT 59.231 33.333 0.00 0.00 33.97 3.32
3288 6040 4.036144 GCAATCTCATTTCTTGGCTACTCC 59.964 45.833 0.00 0.00 0.00 3.85
3398 6152 7.106439 TCACAGAACAATATGTGTGGTTTTT 57.894 32.000 5.34 0.00 46.41 1.94
3424 6178 3.812156 ATCCGTTCCATATTCGTGTGA 57.188 42.857 0.00 0.00 0.00 3.58
3430 6184 6.016192 TCACTCACTCTATCCGTTCCATATTC 60.016 42.308 0.00 0.00 0.00 1.75
3486 6240 5.180117 CACTAGTTGATTCAGTTGGAGGTTG 59.820 44.000 0.00 0.00 0.00 3.77
3515 6269 2.528127 TTGGGGGTCCGCTCTCAA 60.528 61.111 5.82 0.00 35.24 3.02
3523 6279 5.125367 ACTTGATTATTAGTTGGGGGTCC 57.875 43.478 0.00 0.00 0.00 4.46
3568 6328 4.592942 TCACCCTCCATCATCTCAAAAAG 58.407 43.478 0.00 0.00 0.00 2.27
3578 6338 2.502068 ATGGATCTCACCCTCCATCA 57.498 50.000 0.00 0.00 46.95 3.07
3641 6401 3.803082 CAAGGCCCACGCATGTCG 61.803 66.667 0.00 7.79 45.38 4.35
3648 6408 1.080569 GTGATTTGCAAGGCCCACG 60.081 57.895 0.00 0.00 0.00 4.94
3684 6444 3.257624 TGCACACATAATTGACATTGCCA 59.742 39.130 0.00 0.00 0.00 4.92
3698 6458 2.873472 CAAAGCCACAAATTGCACACAT 59.127 40.909 0.00 0.00 0.00 3.21
3731 6491 3.926058 TTAAGCTTCATGGGGGTCTAC 57.074 47.619 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.