Multiple sequence alignment - TraesCS7A01G149000

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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 TraesCS7A01G149000 chr7A 100.000 3672 0 0 1 3672 102291423 102287752 0.000000e+00 6782.0
1 TraesCS7A01G149000 chr7A 90.057 523 37 3 4 523 114106883 114107393 0.000000e+00 664.0
2 TraesCS7A01G149000 chr7A 90.741 54 5 0 1047 1100 577206144 577206197 5.090000e-09 73.1
3 TraesCS7A01G149000 chr7B 91.738 1525 67 25 1562 3066 55035258 55033773 0.000000e+00 2063.0
4 TraesCS7A01G149000 chr7B 87.213 1001 54 31 586 1541 55036323 55035352 0.000000e+00 1072.0
5 TraesCS7A01G149000 chr7B 90.530 792 52 11 1562 2342 55066414 55065635 0.000000e+00 1026.0
6 TraesCS7A01G149000 chr7B 84.689 627 68 7 3069 3672 55033674 55033053 5.250000e-168 601.0
7 TraesCS7A01G149000 chr7B 94.805 231 12 0 2479 2709 55065514 55065284 9.690000e-96 361.0
8 TraesCS7A01G149000 chr7B 83.923 311 21 17 1231 1524 55066940 55066642 1.680000e-68 270.0
9 TraesCS7A01G149000 chr7B 94.479 163 3 1 992 1154 55067146 55066990 2.830000e-61 246.0
10 TraesCS7A01G149000 chr7B 90.741 54 5 0 1047 1100 535697472 535697525 5.090000e-09 73.1
11 TraesCS7A01G149000 chr7D 90.497 926 32 20 586 1492 99824676 99823788 0.000000e+00 1171.0
12 TraesCS7A01G149000 chr7D 93.185 807 27 11 1562 2347 99873627 99872828 0.000000e+00 1160.0
13 TraesCS7A01G149000 chr7D 94.051 706 27 8 1592 2285 99823618 99822916 0.000000e+00 1057.0
14 TraesCS7A01G149000 chr7D 88.060 871 58 23 2400 3251 99822874 99822031 0.000000e+00 990.0
15 TraesCS7A01G149000 chr7D 87.440 621 42 20 934 1541 99874319 99873722 0.000000e+00 682.0
16 TraesCS7A01G149000 chr7D 92.683 246 12 4 2476 2718 99872710 99872468 2.100000e-92 350.0
17 TraesCS7A01G149000 chr7D 95.652 69 3 0 1473 1541 99823777 99823709 1.080000e-20 111.0
18 TraesCS7A01G149000 chr7D 85.455 55 7 1 1047 1100 507302712 507302766 5.120000e-04 56.5
19 TraesCS7A01G149000 chr7D 100.000 29 0 0 2359 2387 99822902 99822874 2.000000e-03 54.7
20 TraesCS7A01G149000 chr4A 94.815 540 11 5 1 537 377606677 377606152 0.000000e+00 826.0
21 TraesCS7A01G149000 chr4A 82.759 116 17 3 434 547 579522739 579522625 2.330000e-17 100.0
22 TraesCS7A01G149000 chrUn 94.444 540 12 4 1 537 77226182 77226706 0.000000e+00 815.0
23 TraesCS7A01G149000 chr6A 91.810 525 40 2 2 523 129358226 129358750 0.000000e+00 728.0
24 TraesCS7A01G149000 chr2A 91.205 523 32 2 2 521 409198364 409198875 0.000000e+00 699.0
25 TraesCS7A01G149000 chr2A 94.595 407 18 3 132 537 17375893 17375490 8.660000e-176 627.0
26 TraesCS7A01G149000 chr2A 85.468 523 42 13 4 523 625411459 625410968 7.030000e-142 514.0
27 TraesCS7A01G149000 chr4B 80.464 517 75 19 15 522 36787747 36787248 4.480000e-99 372.0
28 TraesCS7A01G149000 chr4B 80.077 517 76 20 16 522 36688805 36688306 3.490000e-95 359.0
29 TraesCS7A01G149000 chr5A 86.598 194 26 0 1638 1831 440262521 440262714 7.990000e-52 215.0
30 TraesCS7A01G149000 chr5B 86.082 194 27 0 1638 1831 398346644 398346837 3.720000e-50 209.0
31 TraesCS7A01G149000 chr5D 85.567 194 28 0 1638 1831 339352917 339353110 1.730000e-48 204.0
32 TraesCS7A01G149000 chr1D 92.857 42 1 2 493 534 123698095 123698134 3.960000e-05 60.2


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 TraesCS7A01G149000 chr7A 102287752 102291423 3671 True 6782.000000 6782 100.000000 1 3672 1 chr7A.!!$R1 3671
1 TraesCS7A01G149000 chr7A 114106883 114107393 510 False 664.000000 664 90.057000 4 523 1 chr7A.!!$F1 519
2 TraesCS7A01G149000 chr7B 55033053 55036323 3270 True 1245.333333 2063 87.880000 586 3672 3 chr7B.!!$R1 3086
3 TraesCS7A01G149000 chr7B 55065284 55067146 1862 True 475.750000 1026 90.934250 992 2709 4 chr7B.!!$R2 1717
4 TraesCS7A01G149000 chr7D 99872468 99874319 1851 True 730.666667 1160 91.102667 934 2718 3 chr7D.!!$R2 1784
5 TraesCS7A01G149000 chr7D 99822031 99824676 2645 True 676.740000 1171 93.652000 586 3251 5 chr7D.!!$R1 2665
6 TraesCS7A01G149000 chr4A 377606152 377606677 525 True 826.000000 826 94.815000 1 537 1 chr4A.!!$R1 536
7 TraesCS7A01G149000 chrUn 77226182 77226706 524 False 815.000000 815 94.444000 1 537 1 chrUn.!!$F1 536
8 TraesCS7A01G149000 chr6A 129358226 129358750 524 False 728.000000 728 91.810000 2 523 1 chr6A.!!$F1 521
9 TraesCS7A01G149000 chr2A 409198364 409198875 511 False 699.000000 699 91.205000 2 521 1 chr2A.!!$F1 519

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
685 703 0.040646 ACCCGGAGTCTACACCATGA 59.959 55.0 0.73 0.0 0.0 3.07 F
2350 2710 0.036952 CATCCCTGTCTCTGTTGCGT 60.037 55.0 0.00 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 2757 0.102663 TACACTTCAACGCGACACCA 59.897 50.0 15.93 0.0 0.00 4.17 R
3417 3966 0.037605 ACTTTTAGGGCACGTCCTCG 60.038 55.0 0.00 0.0 43.34 4.63 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
83 84 4.522722 TCGATAACCACACATACACACA 57.477 40.909 0.00 0.00 0.00 3.72
125 127 6.550854 AGGGAAAAACAACAGATTTCTCATCA 59.449 34.615 0.00 0.00 36.28 3.07
289 294 4.116328 TCGTTGCGAGGGCGAGAG 62.116 66.667 0.00 0.00 44.10 3.20
290 295 4.116328 CGTTGCGAGGGCGAGAGA 62.116 66.667 0.00 0.00 44.10 3.10
291 296 2.202676 GTTGCGAGGGCGAGAGAG 60.203 66.667 0.00 0.00 44.10 3.20
292 297 2.361230 TTGCGAGGGCGAGAGAGA 60.361 61.111 0.00 0.00 44.10 3.10
293 298 2.410687 TTGCGAGGGCGAGAGAGAG 61.411 63.158 0.00 0.00 44.10 3.20
409 426 3.055385 CCGACAAGGGTGAGAAGGATAAA 60.055 47.826 0.00 0.00 35.97 1.40
543 560 6.111768 CACTGACATTTGTGCTATTCCTAC 57.888 41.667 0.00 0.00 0.00 3.18
544 561 5.065218 CACTGACATTTGTGCTATTCCTACC 59.935 44.000 0.00 0.00 0.00 3.18
545 562 5.172687 TGACATTTGTGCTATTCCTACCA 57.827 39.130 0.00 0.00 0.00 3.25
546 563 5.565509 TGACATTTGTGCTATTCCTACCAA 58.434 37.500 0.00 0.00 0.00 3.67
547 564 5.414454 TGACATTTGTGCTATTCCTACCAAC 59.586 40.000 0.00 0.00 0.00 3.77
548 565 5.570320 ACATTTGTGCTATTCCTACCAACT 58.430 37.500 0.00 0.00 0.00 3.16
549 566 5.648092 ACATTTGTGCTATTCCTACCAACTC 59.352 40.000 0.00 0.00 0.00 3.01
550 567 4.901197 TTGTGCTATTCCTACCAACTCA 57.099 40.909 0.00 0.00 0.00 3.41
551 568 4.471904 TGTGCTATTCCTACCAACTCAG 57.528 45.455 0.00 0.00 0.00 3.35
552 569 4.093743 TGTGCTATTCCTACCAACTCAGA 58.906 43.478 0.00 0.00 0.00 3.27
553 570 4.081642 TGTGCTATTCCTACCAACTCAGAC 60.082 45.833 0.00 0.00 0.00 3.51
554 571 4.081642 GTGCTATTCCTACCAACTCAGACA 60.082 45.833 0.00 0.00 0.00 3.41
555 572 4.716784 TGCTATTCCTACCAACTCAGACAT 59.283 41.667 0.00 0.00 0.00 3.06
556 573 5.189736 TGCTATTCCTACCAACTCAGACATT 59.810 40.000 0.00 0.00 0.00 2.71
557 574 6.382859 TGCTATTCCTACCAACTCAGACATTA 59.617 38.462 0.00 0.00 0.00 1.90
558 575 6.926272 GCTATTCCTACCAACTCAGACATTAG 59.074 42.308 0.00 0.00 0.00 1.73
559 576 7.201920 GCTATTCCTACCAACTCAGACATTAGA 60.202 40.741 0.00 0.00 0.00 2.10
560 577 6.928348 TTCCTACCAACTCAGACATTAGAA 57.072 37.500 0.00 0.00 0.00 2.10
561 578 6.282199 TCCTACCAACTCAGACATTAGAAC 57.718 41.667 0.00 0.00 0.00 3.01
562 579 6.017192 TCCTACCAACTCAGACATTAGAACT 58.983 40.000 0.00 0.00 0.00 3.01
563 580 7.179966 TCCTACCAACTCAGACATTAGAACTA 58.820 38.462 0.00 0.00 0.00 2.24
564 581 7.339721 TCCTACCAACTCAGACATTAGAACTAG 59.660 40.741 0.00 0.00 0.00 2.57
565 582 7.339721 CCTACCAACTCAGACATTAGAACTAGA 59.660 40.741 0.00 0.00 0.00 2.43
566 583 7.540474 ACCAACTCAGACATTAGAACTAGAA 57.460 36.000 0.00 0.00 0.00 2.10
567 584 8.140112 ACCAACTCAGACATTAGAACTAGAAT 57.860 34.615 0.00 0.00 0.00 2.40
568 585 9.256228 ACCAACTCAGACATTAGAACTAGAATA 57.744 33.333 0.00 0.00 0.00 1.75
615 632 1.807377 GCCCAAATCCAAATGCATCCG 60.807 52.381 0.00 0.00 0.00 4.18
682 700 2.280552 GCACCCGGAGTCTACACCA 61.281 63.158 0.73 0.00 0.00 4.17
685 703 0.040646 ACCCGGAGTCTACACCATGA 59.959 55.000 0.73 0.00 0.00 3.07
713 745 9.270640 TGAATGAAAACATCAAAAGTATTTGGG 57.729 29.630 1.86 0.00 44.88 4.12
841 874 3.874543 CTCGCGTGCTCCTCTATCTATAT 59.125 47.826 5.77 0.00 0.00 0.86
845 878 7.215085 TCGCGTGCTCCTCTATCTATATATAA 58.785 38.462 5.77 0.00 0.00 0.98
864 902 1.286501 AGTACGCACACACAACACAG 58.713 50.000 0.00 0.00 0.00 3.66
923 961 3.858877 GCCTGACTAGTTGATATCGCCAG 60.859 52.174 0.00 0.00 0.00 4.85
1242 1320 3.754850 TCGTCGTCTCAATTAACCTCTGA 59.245 43.478 0.00 0.00 0.00 3.27
1435 1513 4.742659 GGTACGTACGTTTAACCTTTGTCA 59.257 41.667 27.92 0.00 0.00 3.58
1466 1544 3.885297 CTCAACCATTATTGCCTTCCGAT 59.115 43.478 0.00 0.00 0.00 4.18
1538 1776 3.614616 CGTTTCTATTCTGACTGGACTGC 59.385 47.826 0.00 0.00 0.00 4.40
1541 1779 3.435275 TCTATTCTGACTGGACTGCACT 58.565 45.455 0.00 0.00 0.00 4.40
1542 1780 2.469274 ATTCTGACTGGACTGCACTG 57.531 50.000 0.00 0.00 0.00 3.66
1831 2167 2.260844 TCTGCAAGAAGACCAAGGTG 57.739 50.000 0.00 0.00 42.31 4.00
1850 2198 4.095610 GGTGCGTTGTAGTATTTTGCATC 58.904 43.478 0.00 0.00 33.01 3.91
1906 2261 1.284982 GATCGTTCTGTGTGCGTGCT 61.285 55.000 0.00 0.00 0.00 4.40
2287 2642 2.952978 CCCAGCAGGTCAGTAGTACTAG 59.047 54.545 1.87 0.00 0.00 2.57
2288 2643 3.622630 CCAGCAGGTCAGTAGTACTAGT 58.377 50.000 1.87 3.18 0.00 2.57
2293 2648 6.542735 CAGCAGGTCAGTAGTACTAGTAATCA 59.457 42.308 6.05 0.00 0.00 2.57
2302 2657 3.889538 AGTACTAGTAATCAGCCATCGCA 59.110 43.478 3.61 0.00 37.52 5.10
2303 2658 3.377346 ACTAGTAATCAGCCATCGCAG 57.623 47.619 0.00 0.00 37.52 5.18
2304 2659 2.064762 CTAGTAATCAGCCATCGCAGC 58.935 52.381 0.00 0.00 37.52 5.25
2305 2660 0.877649 AGTAATCAGCCATCGCAGCG 60.878 55.000 9.06 9.06 37.52 5.18
2347 2707 0.393537 GCCCATCCCTGTCTCTGTTG 60.394 60.000 0.00 0.00 0.00 3.33
2350 2710 0.036952 CATCCCTGTCTCTGTTGCGT 60.037 55.000 0.00 0.00 0.00 5.24
2351 2711 0.687354 ATCCCTGTCTCTGTTGCGTT 59.313 50.000 0.00 0.00 0.00 4.84
2352 2712 0.249868 TCCCTGTCTCTGTTGCGTTG 60.250 55.000 0.00 0.00 0.00 4.10
2353 2713 1.571460 CCTGTCTCTGTTGCGTTGC 59.429 57.895 0.00 0.00 0.00 4.17
2354 2714 1.159713 CCTGTCTCTGTTGCGTTGCA 61.160 55.000 0.00 0.00 36.47 4.08
2355 2715 0.657312 CTGTCTCTGTTGCGTTGCAA 59.343 50.000 0.00 0.00 46.80 4.08
2387 2752 2.139917 GTCAACACACGTGCTAATGGA 58.860 47.619 17.22 3.22 0.00 3.41
2388 2753 2.157668 GTCAACACACGTGCTAATGGAG 59.842 50.000 17.22 3.68 0.00 3.86
2389 2754 2.143122 CAACACACGTGCTAATGGAGT 58.857 47.619 17.22 0.00 0.00 3.85
2390 2755 3.006003 TCAACACACGTGCTAATGGAGTA 59.994 43.478 17.22 0.00 0.00 2.59
2391 2756 3.671008 ACACACGTGCTAATGGAGTAA 57.329 42.857 17.22 0.00 0.00 2.24
2392 2757 4.202245 ACACACGTGCTAATGGAGTAAT 57.798 40.909 17.22 0.00 0.00 1.89
2393 2758 3.932710 ACACACGTGCTAATGGAGTAATG 59.067 43.478 17.22 3.85 0.00 1.90
2394 2759 3.309682 CACACGTGCTAATGGAGTAATGG 59.690 47.826 17.22 0.00 0.00 3.16
2395 2760 3.055385 ACACGTGCTAATGGAGTAATGGT 60.055 43.478 17.22 0.00 0.00 3.55
2396 2761 3.309682 CACGTGCTAATGGAGTAATGGTG 59.690 47.826 0.82 0.00 0.00 4.17
2397 2762 3.055385 ACGTGCTAATGGAGTAATGGTGT 60.055 43.478 0.00 0.00 0.00 4.16
2398 2763 3.555956 CGTGCTAATGGAGTAATGGTGTC 59.444 47.826 0.00 0.00 0.00 3.67
2399 2764 3.555956 GTGCTAATGGAGTAATGGTGTCG 59.444 47.826 0.00 0.00 0.00 4.35
2674 3074 4.267452 GCGATGAAAGAGATCAACTGAGAC 59.733 45.833 0.00 0.00 32.06 3.36
2726 3129 2.294979 CATCCATGCATGCAGTACTGT 58.705 47.619 26.69 4.78 0.00 3.55
2727 3130 3.469739 CATCCATGCATGCAGTACTGTA 58.530 45.455 26.69 20.06 0.00 2.74
2728 3131 3.843893 TCCATGCATGCAGTACTGTAT 57.156 42.857 26.69 21.44 36.33 2.29
2781 3189 2.048023 CGGCATGCCATTCTGGTGT 61.048 57.895 34.93 0.00 40.46 4.16
2783 3191 0.966875 GGCATGCCATTCTGGTGTCA 60.967 55.000 32.08 0.00 40.46 3.58
2902 3333 2.762535 TGCTCCTTGGTAGCACTAAC 57.237 50.000 0.00 0.00 44.78 2.34
2980 3411 2.819115 CTCACAAGTCTCATCCCATCG 58.181 52.381 0.00 0.00 0.00 3.84
3144 3674 1.884067 GCCACCAAAGCTCTAGCAGTT 60.884 52.381 4.54 0.00 45.16 3.16
3207 3737 3.808618 GCACCATGACATCCTAGATTCCC 60.809 52.174 0.00 0.00 0.00 3.97
3228 3758 1.137513 GGCACACGTCACAGTTCTAC 58.862 55.000 0.00 0.00 0.00 2.59
3256 3786 7.603297 TTTATCTTTCTTTTGAAAAGACGCG 57.397 32.000 19.07 3.53 46.42 6.01
3265 3795 3.799137 TGAAAAGACGCGGATAAACAC 57.201 42.857 12.47 0.00 0.00 3.32
3286 3825 3.684788 ACACCGAAAATACAGAGCACATC 59.315 43.478 0.00 0.00 0.00 3.06
3321 3870 4.921470 AATTACATCGACAACTGAACGG 57.079 40.909 0.00 0.00 0.00 4.44
3341 3890 1.070134 GCCTATGCCACCGTCAGAATA 59.930 52.381 0.00 0.00 0.00 1.75
3342 3891 2.868044 GCCTATGCCACCGTCAGAATAG 60.868 54.545 0.00 0.00 0.00 1.73
3345 3894 0.535335 TGCCACCGTCAGAATAGGTC 59.465 55.000 0.00 0.00 35.85 3.85
3349 3898 0.739561 ACCGTCAGAATAGGTCGCTC 59.260 55.000 0.00 0.00 31.69 5.03
3378 3927 1.542472 TCGTTGTCGCTCTCATACCAA 59.458 47.619 0.00 0.00 36.96 3.67
3385 3934 1.020437 GCTCTCATACCAAAGCCAGC 58.980 55.000 0.00 0.00 0.00 4.85
3388 3937 1.065199 TCTCATACCAAAGCCAGCCTG 60.065 52.381 0.00 0.00 0.00 4.85
3394 3943 2.281761 AAAGCCAGCCTGACCACG 60.282 61.111 0.00 0.00 0.00 4.94
3397 3946 4.314440 GCCAGCCTGACCACGTCA 62.314 66.667 0.00 0.00 40.50 4.35
3399 3948 1.003355 CCAGCCTGACCACGTCAAT 60.003 57.895 0.00 0.00 42.26 2.57
3402 3951 0.615331 AGCCTGACCACGTCAATGAT 59.385 50.000 0.00 0.00 42.26 2.45
3409 3958 3.259625 TGACCACGTCAATGATAACTGGA 59.740 43.478 5.75 0.00 39.78 3.86
3415 3964 4.935808 ACGTCAATGATAACTGGAAAGTCC 59.064 41.667 0.00 0.00 36.96 3.85
3417 3966 5.292101 CGTCAATGATAACTGGAAAGTCCTC 59.708 44.000 0.00 0.00 37.46 3.71
3418 3967 5.292101 GTCAATGATAACTGGAAAGTCCTCG 59.708 44.000 0.00 0.00 37.46 4.63
3421 3970 3.447586 TGATAACTGGAAAGTCCTCGAGG 59.552 47.826 26.32 26.32 37.46 4.63
3433 3982 1.601419 CCTCGAGGACGTGCCCTAAA 61.601 60.000 28.21 0.00 40.69 1.85
3436 3985 0.037605 CGAGGACGTGCCCTAAAAGT 60.038 55.000 2.38 0.00 36.49 2.66
3445 3994 0.107165 GCCCTAAAAGTCATCGCCCT 60.107 55.000 0.00 0.00 0.00 5.19
3446 3995 1.682087 GCCCTAAAAGTCATCGCCCTT 60.682 52.381 0.00 0.00 0.00 3.95
3481 4030 8.308931 CCCTTGAATTGAATTTGATCTGAAGAA 58.691 33.333 0.00 0.00 0.00 2.52
3485 4034 8.301720 TGAATTGAATTTGATCTGAAGAACCTG 58.698 33.333 0.00 0.00 0.00 4.00
3496 4045 7.337689 TGATCTGAAGAACCTGATACCAAATTG 59.662 37.037 0.00 0.00 0.00 2.32
3499 4048 3.365472 AGAACCTGATACCAAATTGGCC 58.635 45.455 12.67 0.00 42.67 5.36
3521 4074 2.713967 GCGTACCCTAACCTCGCCA 61.714 63.158 0.00 0.00 40.83 5.69
3526 4079 1.382146 CCCTAACCTCGCCACCCTA 60.382 63.158 0.00 0.00 0.00 3.53
3528 4081 0.906775 CCTAACCTCGCCACCCTAAA 59.093 55.000 0.00 0.00 0.00 1.85
3536 4089 0.893727 CGCCACCCTAAAAAGCCAGT 60.894 55.000 0.00 0.00 0.00 4.00
3542 4095 4.569865 CCACCCTAAAAAGCCAGTAGGAAT 60.570 45.833 0.00 0.00 37.21 3.01
3545 4098 5.729718 ACCCTAAAAAGCCAGTAGGAATCTA 59.270 40.000 0.00 0.00 37.21 1.98
3549 4102 3.778954 AAGCCAGTAGGAATCTATGCC 57.221 47.619 0.00 0.00 36.89 4.40
3550 4103 1.620819 AGCCAGTAGGAATCTATGCCG 59.379 52.381 0.00 0.00 36.89 5.69
3551 4104 1.618837 GCCAGTAGGAATCTATGCCGA 59.381 52.381 0.00 0.00 36.89 5.54
3558 4111 6.984474 CAGTAGGAATCTATGCCGAAGTTTTA 59.016 38.462 0.00 0.00 0.00 1.52
3564 4117 8.188139 GGAATCTATGCCGAAGTTTTATTGAAA 58.812 33.333 0.00 0.00 0.00 2.69
3565 4118 9.736023 GAATCTATGCCGAAGTTTTATTGAAAT 57.264 29.630 0.00 0.00 0.00 2.17
3570 4123 7.778470 TGCCGAAGTTTTATTGAAATTGTTT 57.222 28.000 0.00 0.00 0.00 2.83
3585 4138 6.699642 TGAAATTGTTTCAAAGGACGAATTCC 59.300 34.615 0.00 0.00 45.94 3.01
3595 4148 2.419667 GGACGAATTCCAAAGACCGAA 58.580 47.619 0.00 0.00 45.10 4.30
3609 4162 3.942829 AGACCGAATCAAAGATGAAGCA 58.057 40.909 0.00 0.00 39.49 3.91
3610 4163 3.686726 AGACCGAATCAAAGATGAAGCAC 59.313 43.478 0.00 0.00 39.49 4.40
3611 4164 2.749621 ACCGAATCAAAGATGAAGCACC 59.250 45.455 0.00 0.00 39.49 5.01
3622 4175 3.647649 GAAGCACCGCCATTTGCCC 62.648 63.158 0.00 0.00 39.75 5.36
3626 4179 4.344865 ACCGCCATTTGCCCGAGT 62.345 61.111 0.00 0.00 36.24 4.18
3637 4190 2.037367 CCCGAGTGACCCTCCTGA 59.963 66.667 0.00 0.00 36.82 3.86
3645 4198 3.517500 GAGTGACCCTCCTGAGAGAATTT 59.482 47.826 0.00 0.00 43.39 1.82
3651 4204 4.852697 ACCCTCCTGAGAGAATTTAAACCT 59.147 41.667 0.00 0.00 43.39 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.900601 AGTGGGTGTTTATTTGCAATCCA 59.099 39.130 0.00 0.00 0.00 3.41
83 84 2.162681 CCCTTGCGAGGTTTTTCAGAT 58.837 47.619 19.14 0.00 41.85 2.90
282 287 1.498865 CTCTCGCTCTCTCTCTCGCC 61.499 65.000 0.00 0.00 0.00 5.54
283 288 0.529773 TCTCTCGCTCTCTCTCTCGC 60.530 60.000 0.00 0.00 0.00 5.03
284 289 1.067060 TCTCTCTCGCTCTCTCTCTCG 59.933 57.143 0.00 0.00 0.00 4.04
285 290 2.546795 CCTCTCTCTCGCTCTCTCTCTC 60.547 59.091 0.00 0.00 0.00 3.20
286 291 1.414181 CCTCTCTCTCGCTCTCTCTCT 59.586 57.143 0.00 0.00 0.00 3.10
287 292 1.541233 CCCTCTCTCTCGCTCTCTCTC 60.541 61.905 0.00 0.00 0.00 3.20
288 293 0.469917 CCCTCTCTCTCGCTCTCTCT 59.530 60.000 0.00 0.00 0.00 3.10
289 294 0.535102 CCCCTCTCTCTCGCTCTCTC 60.535 65.000 0.00 0.00 0.00 3.20
290 295 1.531748 CCCCTCTCTCTCGCTCTCT 59.468 63.158 0.00 0.00 0.00 3.10
291 296 1.528309 CCCCCTCTCTCTCGCTCTC 60.528 68.421 0.00 0.00 0.00 3.20
292 297 2.600731 CCCCCTCTCTCTCGCTCT 59.399 66.667 0.00 0.00 0.00 4.09
523 540 5.172687 TGGTAGGAATAGCACAAATGTCA 57.827 39.130 0.00 0.00 0.00 3.58
525 542 5.570320 AGTTGGTAGGAATAGCACAAATGT 58.430 37.500 0.00 0.00 0.00 2.71
537 554 6.497259 AGTTCTAATGTCTGAGTTGGTAGGAA 59.503 38.462 0.00 0.00 0.00 3.36
538 555 6.017192 AGTTCTAATGTCTGAGTTGGTAGGA 58.983 40.000 0.00 0.00 0.00 2.94
539 556 6.287589 AGTTCTAATGTCTGAGTTGGTAGG 57.712 41.667 0.00 0.00 0.00 3.18
540 557 8.282455 TCTAGTTCTAATGTCTGAGTTGGTAG 57.718 38.462 0.00 0.00 0.00 3.18
541 558 8.645814 TTCTAGTTCTAATGTCTGAGTTGGTA 57.354 34.615 0.00 0.00 0.00 3.25
542 559 7.540474 TTCTAGTTCTAATGTCTGAGTTGGT 57.460 36.000 0.00 0.00 0.00 3.67
655 673 1.597027 CTCCGGGTGCACGTTTCTT 60.597 57.895 11.45 0.00 0.00 2.52
713 745 3.206964 GCAGGGCTTTACCAGAAGATAC 58.793 50.000 0.00 0.00 42.05 2.24
716 748 0.328258 GGCAGGGCTTTACCAGAAGA 59.672 55.000 0.00 0.00 42.05 2.87
794 827 1.048601 GGTGGTGGACTTGACAGAGA 58.951 55.000 0.00 0.00 0.00 3.10
841 874 4.618965 TGTGTTGTGTGTGCGTACTTATA 58.381 39.130 4.97 0.00 0.00 0.98
845 878 1.134936 TCTGTGTTGTGTGTGCGTACT 60.135 47.619 4.97 0.00 0.00 2.73
864 902 4.459089 GTGGGGAGCGCTGGTCTC 62.459 72.222 18.48 4.53 0.00 3.36
923 961 5.050091 CGGTTAGGTGAATGAATAGATGTGC 60.050 44.000 0.00 0.00 0.00 4.57
1205 1283 2.287668 ACGACGAGTCAGAAGTCCAAAG 60.288 50.000 0.00 0.00 0.00 2.77
1206 1284 1.679680 ACGACGAGTCAGAAGTCCAAA 59.320 47.619 0.00 0.00 0.00 3.28
1207 1285 1.315690 ACGACGAGTCAGAAGTCCAA 58.684 50.000 0.00 0.00 0.00 3.53
1208 1286 3.016997 ACGACGAGTCAGAAGTCCA 57.983 52.632 0.00 0.00 0.00 4.02
1466 1544 3.885724 TCCACAGCAGTTATCGAATCA 57.114 42.857 0.00 0.00 0.00 2.57
1529 1767 0.767375 ATTGTCCAGTGCAGTCCAGT 59.233 50.000 0.00 0.00 0.00 4.00
1538 1776 3.303990 CGACTTTGACCAATTGTCCAGTG 60.304 47.826 4.43 2.01 43.78 3.66
1541 1779 2.875933 GACGACTTTGACCAATTGTCCA 59.124 45.455 4.43 0.00 43.78 4.02
1542 1780 2.875933 TGACGACTTTGACCAATTGTCC 59.124 45.455 4.43 0.00 43.78 4.02
1609 1930 0.986992 GCACGCACATCAAGATTTGC 59.013 50.000 10.36 10.36 40.17 3.68
1613 1934 2.787249 GCGCACGCACATCAAGAT 59.213 55.556 10.65 0.00 41.49 2.40
1831 2167 4.095610 GTGGATGCAAAATACTACAACGC 58.904 43.478 0.00 0.00 0.00 4.84
1906 2261 5.392703 CGTAGCAGTACCAGTTCTGACATAA 60.393 44.000 8.43 0.00 34.02 1.90
2287 2642 0.875908 TCGCTGCGATGGCTGATTAC 60.876 55.000 22.24 0.00 40.22 1.89
2288 2643 0.598419 CTCGCTGCGATGGCTGATTA 60.598 55.000 26.15 0.00 40.22 1.75
2321 2681 1.763546 GACAGGGATGGGCCTAGCTC 61.764 65.000 3.74 0.00 36.66 4.09
2332 2692 0.687354 AACGCAACAGAGACAGGGAT 59.313 50.000 0.00 0.00 0.00 3.85
2352 2712 1.860326 GTTGACATGGTTGCAAGTTGC 59.140 47.619 21.17 21.17 45.29 4.17
2353 2713 2.859538 GTGTTGACATGGTTGCAAGTTG 59.140 45.455 0.00 0.00 0.00 3.16
2354 2714 2.495270 TGTGTTGACATGGTTGCAAGTT 59.505 40.909 0.00 0.00 0.00 2.66
2355 2715 2.098614 TGTGTTGACATGGTTGCAAGT 58.901 42.857 0.00 0.00 0.00 3.16
2356 2716 2.462889 GTGTGTTGACATGGTTGCAAG 58.537 47.619 0.00 0.00 33.63 4.01
2387 2752 2.066262 CTTCAACGCGACACCATTACT 58.934 47.619 15.93 0.00 0.00 2.24
2388 2753 1.796459 ACTTCAACGCGACACCATTAC 59.204 47.619 15.93 0.00 0.00 1.89
2389 2754 1.795872 CACTTCAACGCGACACCATTA 59.204 47.619 15.93 0.00 0.00 1.90
2390 2755 0.586319 CACTTCAACGCGACACCATT 59.414 50.000 15.93 0.00 0.00 3.16
2391 2756 0.531974 ACACTTCAACGCGACACCAT 60.532 50.000 15.93 0.00 0.00 3.55
2392 2757 0.102663 TACACTTCAACGCGACACCA 59.897 50.000 15.93 0.00 0.00 4.17
2393 2758 0.782384 CTACACTTCAACGCGACACC 59.218 55.000 15.93 0.00 0.00 4.16
2394 2759 1.762419 TCTACACTTCAACGCGACAC 58.238 50.000 15.93 0.00 0.00 3.67
2395 2760 2.495409 TTCTACACTTCAACGCGACA 57.505 45.000 15.93 0.00 0.00 4.35
2396 2761 4.385244 AAATTCTACACTTCAACGCGAC 57.615 40.909 15.93 0.00 0.00 5.19
2397 2762 4.508492 TCAAAATTCTACACTTCAACGCGA 59.492 37.500 15.93 0.00 0.00 5.87
2398 2763 4.768145 TCAAAATTCTACACTTCAACGCG 58.232 39.130 3.53 3.53 0.00 6.01
2399 2764 5.748592 ACTCAAAATTCTACACTTCAACGC 58.251 37.500 0.00 0.00 0.00 4.84
2716 3119 6.041423 CATCCATGGATATACAGTACTGCA 57.959 41.667 26.87 10.92 32.93 4.41
2751 3154 0.445436 GCATGCCGATACATAGCTGC 59.555 55.000 6.36 0.00 0.00 5.25
2781 3189 2.146342 GTTTGAGCAACAGCTAGCTGA 58.854 47.619 43.42 22.54 46.30 4.26
2783 3191 2.260844 TGTTTGAGCAACAGCTAGCT 57.739 45.000 12.68 12.68 40.71 3.32
2816 3247 1.667724 CCTTTCCGAACTGCATGCTAG 59.332 52.381 20.33 16.29 0.00 3.42
2868 3299 0.391130 GAGCACAGCGTCCCACATTA 60.391 55.000 0.00 0.00 0.00 1.90
2871 3302 4.314440 GGAGCACAGCGTCCCACA 62.314 66.667 0.00 0.00 0.00 4.17
2872 3303 3.537206 AAGGAGCACAGCGTCCCAC 62.537 63.158 0.00 0.00 32.70 4.61
2902 3333 4.196971 TGTCATTCATGGATGCTTCTGAG 58.803 43.478 9.33 0.00 0.00 3.35
3021 3452 2.202987 GCGTGGATGCAGGAGGAG 60.203 66.667 11.38 0.00 34.15 3.69
3022 3453 3.785859 GGCGTGGATGCAGGAGGA 61.786 66.667 11.38 0.00 36.28 3.71
3023 3454 3.746949 GAGGCGTGGATGCAGGAGG 62.747 68.421 11.38 0.00 36.28 4.30
3072 3602 3.589654 TTCTTCAGAGGGCGCCACG 62.590 63.158 30.85 13.16 0.00 4.94
3113 3643 0.685785 TTTGGTGGCTGCTGGTTGAA 60.686 50.000 0.00 0.00 0.00 2.69
3114 3644 1.076412 TTTGGTGGCTGCTGGTTGA 60.076 52.632 0.00 0.00 0.00 3.18
3115 3645 1.364901 CTTTGGTGGCTGCTGGTTG 59.635 57.895 0.00 0.00 0.00 3.77
3116 3646 2.501602 GCTTTGGTGGCTGCTGGTT 61.502 57.895 0.00 0.00 0.00 3.67
3117 3647 2.914097 GCTTTGGTGGCTGCTGGT 60.914 61.111 0.00 0.00 0.00 4.00
3118 3648 2.599578 AGCTTTGGTGGCTGCTGG 60.600 61.111 0.00 0.00 38.73 4.85
3144 3674 1.408266 GGAGAGGCCAAGGCGAAATTA 60.408 52.381 5.01 0.00 43.06 1.40
3167 3697 3.499737 GGCACGATGCGGGTTCTG 61.500 66.667 0.00 0.00 46.21 3.02
3207 3737 0.530650 AGAACTGTGACGTGTGCCTG 60.531 55.000 0.00 0.00 0.00 4.85
3228 3758 9.815532 CGTCTTTTCAAAAGAAAGATAAAAACG 57.184 29.630 14.32 6.59 42.95 3.60
3256 3786 6.674760 GCTCTGTATTTTCGGTGTGTTTATCC 60.675 42.308 0.00 0.00 0.00 2.59
3265 3795 3.684305 TGATGTGCTCTGTATTTTCGGTG 59.316 43.478 0.00 0.00 0.00 4.94
3321 3870 0.179045 ATTCTGACGGTGGCATAGGC 60.179 55.000 0.00 0.00 40.13 3.93
3349 3898 3.071459 GCGACAACGACGGCTCATG 62.071 63.158 0.00 0.00 42.66 3.07
3355 3904 0.098200 TATGAGAGCGACAACGACGG 59.902 55.000 0.00 0.00 42.66 4.79
3356 3905 1.181001 GTATGAGAGCGACAACGACG 58.819 55.000 0.00 0.00 42.66 5.12
3359 3908 1.990799 TTGGTATGAGAGCGACAACG 58.009 50.000 0.00 0.00 42.93 4.10
3361 3910 2.346803 GCTTTGGTATGAGAGCGACAA 58.653 47.619 0.00 0.00 0.00 3.18
3362 3911 1.405526 GGCTTTGGTATGAGAGCGACA 60.406 52.381 0.00 0.00 36.02 4.35
3378 3927 3.537206 GACGTGGTCAGGCTGGCTT 62.537 63.158 19.90 0.68 32.09 4.35
3385 3934 3.618594 CAGTTATCATTGACGTGGTCAGG 59.381 47.826 0.00 0.00 43.69 3.86
3388 3937 3.857052 TCCAGTTATCATTGACGTGGTC 58.143 45.455 0.00 0.00 0.00 4.02
3394 3943 5.292101 CGAGGACTTTCCAGTTATCATTGAC 59.708 44.000 0.00 0.00 39.61 3.18
3397 3946 5.395768 CCTCGAGGACTTTCCAGTTATCATT 60.396 44.000 28.21 0.00 39.61 2.57
3399 3948 3.447586 CCTCGAGGACTTTCCAGTTATCA 59.552 47.826 28.21 0.00 39.61 2.15
3402 3951 3.165087 TCCTCGAGGACTTTCCAGTTA 57.835 47.619 30.49 3.25 39.61 2.24
3415 3964 0.245539 TTTTAGGGCACGTCCTCGAG 59.754 55.000 5.13 5.13 40.62 4.04
3417 3966 0.037605 ACTTTTAGGGCACGTCCTCG 60.038 55.000 0.00 0.00 43.34 4.63
3418 3967 1.001633 TGACTTTTAGGGCACGTCCTC 59.998 52.381 0.00 0.00 38.30 3.71
3421 3970 1.659098 CGATGACTTTTAGGGCACGTC 59.341 52.381 0.00 0.00 0.00 4.34
3433 3982 3.695830 TCAACTTAAGGGCGATGACTT 57.304 42.857 7.53 0.00 0.00 3.01
3436 3985 2.617021 GGGTTCAACTTAAGGGCGATGA 60.617 50.000 7.53 0.81 0.00 2.92
3445 3994 9.323985 CAAATTCAATTCAAGGGTTCAACTTAA 57.676 29.630 0.00 0.00 0.00 1.85
3446 3995 8.700051 TCAAATTCAATTCAAGGGTTCAACTTA 58.300 29.630 0.00 0.00 0.00 2.24
3481 4030 1.762708 CGGCCAATTTGGTATCAGGT 58.237 50.000 16.62 0.00 40.46 4.00
3485 4034 1.358759 CGGCGGCCAATTTGGTATC 59.641 57.895 20.71 6.43 40.46 2.24
3499 4048 3.763127 GAGGTTAGGGTACGCGGCG 62.763 68.421 22.36 22.36 0.00 6.46
3505 4054 1.519246 GGTGGCGAGGTTAGGGTAC 59.481 63.158 0.00 0.00 0.00 3.34
3521 4074 4.540502 AGATTCCTACTGGCTTTTTAGGGT 59.459 41.667 0.00 0.00 34.23 4.34
3526 4079 4.889995 GGCATAGATTCCTACTGGCTTTTT 59.110 41.667 0.00 0.00 32.10 1.94
3528 4081 3.495100 CGGCATAGATTCCTACTGGCTTT 60.495 47.826 0.00 0.00 32.36 3.51
3536 4089 8.208224 TCAATAAAACTTCGGCATAGATTCCTA 58.792 33.333 0.00 0.00 0.00 2.94
3542 4095 8.519526 ACAATTTCAATAAAACTTCGGCATAGA 58.480 29.630 0.00 0.00 0.00 1.98
3545 4098 7.961325 AACAATTTCAATAAAACTTCGGCAT 57.039 28.000 0.00 0.00 0.00 4.40
3582 4135 5.312895 TCATCTTTGATTCGGTCTTTGGAA 58.687 37.500 0.00 0.00 0.00 3.53
3585 4138 5.091431 GCTTCATCTTTGATTCGGTCTTTG 58.909 41.667 0.00 0.00 0.00 2.77
3595 4148 1.098050 GGCGGTGCTTCATCTTTGAT 58.902 50.000 0.00 0.00 0.00 2.57
3609 4162 4.344865 ACTCGGGCAAATGGCGGT 62.345 61.111 12.93 4.31 46.16 5.68
3610 4163 3.814268 CACTCGGGCAAATGGCGG 61.814 66.667 8.02 8.02 46.16 6.13
3611 4164 2.745884 TCACTCGGGCAAATGGCG 60.746 61.111 0.56 0.00 46.16 5.69
3626 4179 5.280521 GGTTTAAATTCTCTCAGGAGGGTCA 60.281 44.000 0.00 0.00 39.86 4.02
3645 4198 8.284435 TCTGGCTAGTAGATAGGTTAAGGTTTA 58.716 37.037 0.00 0.00 31.55 2.01


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

AutoCloner maintained by Alex Coulton.