Multiple sequence alignment - TraesCS5B01G303900

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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 TraesCS5B01G303900 chr5B 100.000 2390 0 0 1 2390 488112845 488115234 0.000000e+00 4414
1 TraesCS5B01G303900 chr5B 94.687 527 22 3 1 527 488016077 488016597 0.000000e+00 813
2 TraesCS5B01G303900 chr5A 86.876 1623 104 43 820 2390 512619082 512620647 0.000000e+00 1716
3 TraesCS5B01G303900 chr5A 94.140 529 24 6 1 525 512601263 512601788 0.000000e+00 798
4 TraesCS5B01G303900 chr5A 90.414 532 38 6 1 525 512459890 512460415 0.000000e+00 688
5 TraesCS5B01G303900 chr5A 82.927 287 31 11 2106 2390 512625934 512626204 2.370000e-60 243
6 TraesCS5B01G303900 chr5A 82.456 171 12 8 595 765 512604779 512604931 1.490000e-27 134
7 TraesCS5B01G303900 chr5D 90.361 664 31 15 1575 2234 407014004 407013370 0.000000e+00 841
8 TraesCS5B01G303900 chr5D 88.559 708 46 16 886 1573 407014739 407014047 0.000000e+00 826
9 TraesCS5B01G303900 chr5D 93.433 533 28 7 1 527 407020293 407019762 0.000000e+00 784
10 TraesCS5B01G303900 chr5D 89.464 522 47 5 4 525 407106859 407106346 0.000000e+00 652
11 TraesCS5B01G303900 chr5D 86.957 207 22 4 2189 2390 406974359 406974153 6.650000e-56 228
12 TraesCS5B01G303900 chr2D 82.911 474 75 6 15 483 28896263 28896735 2.840000e-114 422
13 TraesCS5B01G303900 chr4B 87.131 373 34 8 912 1270 185241057 185240685 6.150000e-111 411
14 TraesCS5B01G303900 chr4B 83.904 292 39 3 987 1270 672244142 672243851 3.030000e-69 272
15 TraesCS5B01G303900 chr4A 87.131 373 34 7 912 1270 448509059 448509431 6.150000e-111 411
16 TraesCS5B01G303900 chr2B 82.278 474 79 5 15 483 46673104 46673577 2.860000e-109 405
17 TraesCS5B01G303900 chr4D 86.595 373 36 7 912 1270 122206118 122205746 1.330000e-107 399
18 TraesCS5B01G303900 chr2A 84.596 396 61 0 35 430 30766006 30766401 6.190000e-106 394
19 TraesCS5B01G303900 chr2A 83.693 417 65 3 15 428 30858524 30858940 8.010000e-105 390
20 TraesCS5B01G303900 chr7A 84.677 372 46 5 907 1270 213114639 213114271 6.280000e-96 361
21 TraesCS5B01G303900 chr7B 84.682 346 45 3 933 1270 171984449 171984794 2.940000e-89 339
22 TraesCS5B01G303900 chrUn 81.421 366 48 9 913 1270 100076686 100077039 5.030000e-72 281


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 TraesCS5B01G303900 chr5B 488112845 488115234 2389 False 4414.0 4414 100.000 1 2390 1 chr5B.!!$F2 2389
1 TraesCS5B01G303900 chr5B 488016077 488016597 520 False 813.0 813 94.687 1 527 1 chr5B.!!$F1 526
2 TraesCS5B01G303900 chr5A 512619082 512620647 1565 False 1716.0 1716 86.876 820 2390 1 chr5A.!!$F2 1570
3 TraesCS5B01G303900 chr5A 512459890 512460415 525 False 688.0 688 90.414 1 525 1 chr5A.!!$F1 524
4 TraesCS5B01G303900 chr5A 512601263 512604931 3668 False 466.0 798 88.298 1 765 2 chr5A.!!$F4 764
5 TraesCS5B01G303900 chr5D 407013370 407014739 1369 True 833.5 841 89.460 886 2234 2 chr5D.!!$R4 1348
6 TraesCS5B01G303900 chr5D 407019762 407020293 531 True 784.0 784 93.433 1 527 1 chr5D.!!$R2 526
7 TraesCS5B01G303900 chr5D 407106346 407106859 513 True 652.0 652 89.464 4 525 1 chr5D.!!$R3 521

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
817 3754 0.028637 GAATCCGAGTACGTCCCGTC 59.971 60.0 0.0 0.0 41.54 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 4788 0.375106 GGCTACAAGTCGCATGCTTC 59.625 55.0 17.13 8.46 0.0 3.86 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
78 79 0.524862 TCTACTTCGAGAACGTGGGC 59.475 55.000 0.00 0.00 40.69 5.36
115 116 1.338105 CGGTGCTTCTCAACATGAGGA 60.338 52.381 0.00 0.00 44.39 3.71
236 237 0.833287 ATGGAGGGGTTCATCGTGAG 59.167 55.000 0.00 0.00 0.00 3.51
346 347 2.279784 GCATCGAGAGCTTCCCGG 60.280 66.667 0.00 0.00 0.00 5.73
454 462 2.025155 TCCTGGATCGAGAAGTACTGC 58.975 52.381 6.27 0.00 0.00 4.40
457 465 1.135139 TGGATCGAGAAGTACTGCTGC 59.865 52.381 8.55 0.00 0.00 5.25
483 491 5.746245 CGTTCAGAGACCAGAATTCAGATAC 59.254 44.000 8.44 0.00 0.00 2.24
484 492 6.625960 CGTTCAGAGACCAGAATTCAGATACA 60.626 42.308 8.44 0.00 0.00 2.29
485 493 6.462552 TCAGAGACCAGAATTCAGATACAG 57.537 41.667 8.44 0.00 0.00 2.74
486 494 5.954752 TCAGAGACCAGAATTCAGATACAGT 59.045 40.000 8.44 0.00 0.00 3.55
487 495 7.119387 TCAGAGACCAGAATTCAGATACAGTA 58.881 38.462 8.44 0.00 0.00 2.74
491 507 9.853555 GAGACCAGAATTCAGATACAGTATATG 57.146 37.037 8.44 8.68 0.00 1.78
512 528 0.896226 AGAGAAGTACTTGGTCCGGC 59.104 55.000 14.14 0.00 0.00 6.13
515 531 1.697982 AGAAGTACTTGGTCCGGCTTT 59.302 47.619 14.14 0.00 0.00 3.51
561 625 8.348507 GGAAGCTGGAATGAACTATAATCTTTG 58.651 37.037 0.00 0.00 0.00 2.77
566 630 8.383318 TGGAATGAACTATAATCTTTGCTAGC 57.617 34.615 8.10 8.10 0.00 3.42
567 631 8.213679 TGGAATGAACTATAATCTTTGCTAGCT 58.786 33.333 17.23 0.00 0.00 3.32
568 632 9.712305 GGAATGAACTATAATCTTTGCTAGCTA 57.288 33.333 17.23 5.31 0.00 3.32
618 3555 2.540383 TGGTACTCATCCTGCACTCTT 58.460 47.619 0.00 0.00 0.00 2.85
643 3580 2.203684 CCCAGCAAAGGGCCAGTT 60.204 61.111 6.18 0.00 46.50 3.16
657 3594 0.096976 CCAGTTTAGGCGACGCATTG 59.903 55.000 23.09 9.57 0.00 2.82
660 3597 2.607635 CAGTTTAGGCGACGCATTGTAT 59.392 45.455 23.09 0.00 0.00 2.29
661 3598 3.799963 CAGTTTAGGCGACGCATTGTATA 59.200 43.478 23.09 0.00 0.00 1.47
671 3608 5.320723 CGACGCATTGTATAACACACAAAT 58.679 37.500 0.00 0.00 39.22 2.32
677 3614 8.483218 CGCATTGTATAACACACAAATTTTGAA 58.517 29.630 15.81 0.00 39.22 2.69
687 3624 8.647143 ACACACAAATTTTGAATTACAGAAGG 57.353 30.769 15.81 0.00 0.00 3.46
688 3625 7.710475 ACACACAAATTTTGAATTACAGAAGGG 59.290 33.333 15.81 0.00 0.00 3.95
689 3626 7.925483 CACACAAATTTTGAATTACAGAAGGGA 59.075 33.333 15.81 0.00 0.00 4.20
690 3627 8.650490 ACACAAATTTTGAATTACAGAAGGGAT 58.350 29.630 15.81 0.00 0.00 3.85
691 3628 9.143631 CACAAATTTTGAATTACAGAAGGGATC 57.856 33.333 15.81 0.00 0.00 3.36
692 3629 8.314021 ACAAATTTTGAATTACAGAAGGGATCC 58.686 33.333 15.81 1.92 0.00 3.36
693 3630 7.423844 AATTTTGAATTACAGAAGGGATCCC 57.576 36.000 24.59 24.59 0.00 3.85
700 3637 5.630415 TTACAGAAGGGATCCCATTACAG 57.370 43.478 32.69 18.12 38.92 2.74
704 3641 4.884164 CAGAAGGGATCCCATTACAGAAAC 59.116 45.833 32.69 6.27 38.92 2.78
706 3643 5.194537 AGAAGGGATCCCATTACAGAAACAT 59.805 40.000 32.69 3.83 38.92 2.71
707 3644 6.389869 AGAAGGGATCCCATTACAGAAACATA 59.610 38.462 32.69 0.00 38.92 2.29
758 3695 6.479006 TCTTCACAGAGAAATCAATGACCAT 58.521 36.000 0.00 0.00 35.40 3.55
759 3696 6.373495 TCTTCACAGAGAAATCAATGACCATG 59.627 38.462 0.00 0.00 35.40 3.66
760 3697 5.807909 TCACAGAGAAATCAATGACCATGA 58.192 37.500 0.00 0.00 0.00 3.07
761 3698 5.645067 TCACAGAGAAATCAATGACCATGAC 59.355 40.000 0.00 0.00 0.00 3.06
763 3700 6.150641 CACAGAGAAATCAATGACCATGACTT 59.849 38.462 0.00 0.00 0.00 3.01
764 3701 6.150641 ACAGAGAAATCAATGACCATGACTTG 59.849 38.462 0.00 0.00 0.00 3.16
765 3702 5.125097 AGAGAAATCAATGACCATGACTTGC 59.875 40.000 0.00 0.00 0.00 4.01
766 3703 4.768448 AGAAATCAATGACCATGACTTGCA 59.232 37.500 0.00 0.00 0.00 4.08
767 3704 4.713824 AATCAATGACCATGACTTGCAG 57.286 40.909 0.00 0.00 0.00 4.41
768 3705 2.439409 TCAATGACCATGACTTGCAGG 58.561 47.619 0.00 0.00 0.00 4.85
772 3709 3.136123 CCATGACTTGCAGGGCCG 61.136 66.667 0.00 0.00 42.18 6.13
773 3710 3.136123 CATGACTTGCAGGGCCGG 61.136 66.667 0.00 0.00 0.00 6.13
774 3711 4.431131 ATGACTTGCAGGGCCGGG 62.431 66.667 2.18 0.00 0.00 5.73
776 3713 4.660938 GACTTGCAGGGCCGGGTT 62.661 66.667 2.18 0.00 0.00 4.11
777 3714 3.253838 ACTTGCAGGGCCGGGTTA 61.254 61.111 2.18 0.00 0.00 2.85
778 3715 2.438434 CTTGCAGGGCCGGGTTAG 60.438 66.667 2.18 0.00 0.00 2.34
779 3716 4.733542 TTGCAGGGCCGGGTTAGC 62.734 66.667 2.18 1.62 0.00 3.09
781 3718 3.476419 GCAGGGCCGGGTTAGCTA 61.476 66.667 2.18 0.00 0.00 3.32
782 3719 2.504519 CAGGGCCGGGTTAGCTAC 59.495 66.667 2.18 0.00 0.00 3.58
783 3720 2.767073 AGGGCCGGGTTAGCTACC 60.767 66.667 2.18 0.00 46.99 3.18
793 3730 3.162202 GGTTAGCTACCGAAGAGAACC 57.838 52.381 0.00 0.00 37.12 3.62
794 3731 2.759535 GGTTAGCTACCGAAGAGAACCT 59.240 50.000 0.00 0.00 37.98 3.50
795 3732 3.195182 GGTTAGCTACCGAAGAGAACCTT 59.805 47.826 0.00 0.00 37.98 3.50
796 3733 4.422840 GTTAGCTACCGAAGAGAACCTTC 58.577 47.826 0.00 0.00 46.05 3.46
806 3743 4.464069 AAGAGAACCTTCAGAATCCGAG 57.536 45.455 0.00 0.00 0.00 4.63
807 3744 3.436243 AGAGAACCTTCAGAATCCGAGT 58.564 45.455 0.00 0.00 0.00 4.18
808 3745 4.601084 AGAGAACCTTCAGAATCCGAGTA 58.399 43.478 0.00 0.00 0.00 2.59
809 3746 4.399934 AGAGAACCTTCAGAATCCGAGTAC 59.600 45.833 0.00 0.00 0.00 2.73
810 3747 3.128938 AGAACCTTCAGAATCCGAGTACG 59.871 47.826 0.00 0.00 39.43 3.67
811 3748 2.444421 ACCTTCAGAATCCGAGTACGT 58.556 47.619 0.00 0.00 37.88 3.57
812 3749 2.422832 ACCTTCAGAATCCGAGTACGTC 59.577 50.000 0.00 0.00 37.88 4.34
813 3750 2.223525 CCTTCAGAATCCGAGTACGTCC 60.224 54.545 0.00 0.00 37.88 4.79
814 3751 1.386533 TCAGAATCCGAGTACGTCCC 58.613 55.000 0.00 0.00 37.88 4.46
815 3752 0.029035 CAGAATCCGAGTACGTCCCG 59.971 60.000 0.00 0.00 37.88 5.14
816 3753 0.393537 AGAATCCGAGTACGTCCCGT 60.394 55.000 0.00 0.00 44.35 5.28
817 3754 0.028637 GAATCCGAGTACGTCCCGTC 59.971 60.000 0.00 0.00 41.54 4.79
818 3755 1.709147 AATCCGAGTACGTCCCGTCG 61.709 60.000 0.00 0.00 41.54 5.12
837 3774 1.066587 GCCGTCTCCAGAATCCGAG 59.933 63.158 0.00 0.00 0.00 4.63
839 3776 1.323412 CCGTCTCCAGAATCCGAGAT 58.677 55.000 1.65 0.00 37.46 2.75
840 3777 1.683917 CCGTCTCCAGAATCCGAGATT 59.316 52.381 1.65 0.00 37.46 2.40
841 3778 2.544694 CCGTCTCCAGAATCCGAGATTG 60.545 54.545 4.18 0.00 37.46 2.67
842 3779 2.099921 CGTCTCCAGAATCCGAGATTGT 59.900 50.000 4.18 0.00 37.46 2.71
843 3780 3.315470 CGTCTCCAGAATCCGAGATTGTA 59.685 47.826 4.18 0.00 37.46 2.41
844 3781 4.022762 CGTCTCCAGAATCCGAGATTGTAT 60.023 45.833 4.18 0.00 37.46 2.29
845 3782 5.181433 CGTCTCCAGAATCCGAGATTGTATA 59.819 44.000 4.18 0.00 37.46 1.47
858 3795 5.345202 CGAGATTGTATAGTATGCGTTTCCC 59.655 44.000 0.00 0.00 0.00 3.97
876 3813 1.170290 CCCGGCTTCCGTTTTCAACT 61.170 55.000 0.00 0.00 46.80 3.16
877 3814 0.040425 CCGGCTTCCGTTTTCAACTG 60.040 55.000 4.47 0.00 46.80 3.16
878 3815 0.040425 CGGCTTCCGTTTTCAACTGG 60.040 55.000 0.00 0.00 42.73 4.00
879 3816 0.313987 GGCTTCCGTTTTCAACTGGG 59.686 55.000 0.00 0.00 0.00 4.45
880 3817 1.029681 GCTTCCGTTTTCAACTGGGT 58.970 50.000 0.00 0.00 0.00 4.51
881 3818 1.407618 GCTTCCGTTTTCAACTGGGTT 59.592 47.619 0.00 0.00 0.00 4.11
883 3820 3.677700 GCTTCCGTTTTCAACTGGGTTTT 60.678 43.478 0.00 0.00 0.00 2.43
884 3821 4.500127 CTTCCGTTTTCAACTGGGTTTTT 58.500 39.130 0.00 0.00 0.00 1.94
927 3874 1.338107 AAACTAGGGTTTTGCCTGCC 58.662 50.000 0.00 0.00 42.28 4.85
928 3875 0.893727 AACTAGGGTTTTGCCTGCCG 60.894 55.000 0.00 0.00 37.43 5.69
929 3876 1.002624 CTAGGGTTTTGCCTGCCGA 60.003 57.895 0.00 0.00 37.43 5.54
930 3877 1.302993 TAGGGTTTTGCCTGCCGAC 60.303 57.895 0.00 0.00 37.43 4.79
1071 4019 3.887110 TCAACTACTTCGAGTCCAAGTCA 59.113 43.478 6.40 0.00 35.63 3.41
1072 4020 4.523173 TCAACTACTTCGAGTCCAAGTCAT 59.477 41.667 6.40 0.00 35.63 3.06
1073 4021 4.442375 ACTACTTCGAGTCCAAGTCATG 57.558 45.455 6.40 2.31 35.63 3.07
1094 4057 3.745803 GTCGTCGTCGAGCCCCTT 61.746 66.667 4.68 0.00 46.96 3.95
1098 4061 2.036098 TCGTCGAGCCCCTTGGTA 59.964 61.111 0.00 0.00 0.00 3.25
1105 4068 4.462280 GCCCCTTGGTACCCGTCG 62.462 72.222 10.07 0.00 0.00 5.12
1195 4161 3.126879 CCGATTCGCAGCTTGGCA 61.127 61.111 0.00 0.00 0.00 4.92
1277 4243 3.953652 TGGGGAAGGAGGAGGCCA 61.954 66.667 5.01 0.00 0.00 5.36
1288 4257 2.357517 GAGGCCATCGGGTATGCG 60.358 66.667 5.01 0.00 36.17 4.73
1327 4296 2.771328 CTTGCCTTCGCTCCCCCTTT 62.771 60.000 0.00 0.00 35.36 3.11
1333 4302 0.965363 TTCGCTCCCCCTTTTGATGC 60.965 55.000 0.00 0.00 0.00 3.91
1340 4309 3.696548 CTCCCCCTTTTGATGCTAGTTTC 59.303 47.826 0.00 0.00 0.00 2.78
1347 4316 5.705441 CCTTTTGATGCTAGTTTCTACCACA 59.295 40.000 0.00 0.00 0.00 4.17
1350 4319 4.820897 TGATGCTAGTTTCTACCACACTG 58.179 43.478 0.00 0.00 0.00 3.66
1400 4369 9.726232 GATCGGTAAAGTTTAAGTGAAAAGTTT 57.274 29.630 0.00 7.17 42.08 2.66
1403 4372 9.442033 CGGTAAAGTTTAAGTGAAAAGTTTAGG 57.558 33.333 8.76 3.18 41.46 2.69
1426 4395 3.909732 TCTCTTTGGTGGTTTCAATGGT 58.090 40.909 0.00 0.00 0.00 3.55
1433 4402 2.554032 GGTGGTTTCAATGGTGAGTGAG 59.446 50.000 0.00 0.00 34.49 3.51
1450 4419 7.196331 GTGAGTGAGATTAAGCTTGTGTTTTT 58.804 34.615 9.86 0.00 0.00 1.94
1490 4459 2.537625 GACAGTAAGCACGAGATGATGC 59.462 50.000 0.00 0.00 42.39 3.91
1491 4460 2.094026 ACAGTAAGCACGAGATGATGCA 60.094 45.455 0.00 0.00 44.59 3.96
1492 4461 2.931969 CAGTAAGCACGAGATGATGCAA 59.068 45.455 0.00 0.00 44.59 4.08
1493 4462 3.001026 CAGTAAGCACGAGATGATGCAAG 59.999 47.826 0.00 0.00 44.59 4.01
1527 4497 8.251026 TCTGTGACTTATGTGGTAATCTTGTAG 58.749 37.037 0.00 0.00 0.00 2.74
1528 4498 7.903145 TGTGACTTATGTGGTAATCTTGTAGT 58.097 34.615 0.00 0.00 0.00 2.73
1529 4499 9.027202 TGTGACTTATGTGGTAATCTTGTAGTA 57.973 33.333 0.00 0.00 0.00 1.82
1530 4500 9.517609 GTGACTTATGTGGTAATCTTGTAGTAG 57.482 37.037 0.00 0.00 0.00 2.57
1573 4543 5.008415 CACATGTTAATCCATTGGAGAGAGC 59.992 44.000 11.78 1.89 34.05 4.09
1639 4650 5.818336 TGTCAATCAGTTTTCGGTTTGTCTA 59.182 36.000 0.00 0.00 0.00 2.59
1641 4652 6.631636 GTCAATCAGTTTTCGGTTTGTCTAAC 59.368 38.462 0.00 0.00 35.94 2.34
1659 4670 2.825086 ACTCGCCGTCAAATTTATGC 57.175 45.000 0.00 0.00 0.00 3.14
1676 4691 1.153086 GCCTATGGCCAGTCCTGTG 60.153 63.158 13.05 0.00 44.06 3.66
1680 4695 0.327924 TATGGCCAGTCCTGTGTTGG 59.672 55.000 13.05 0.00 35.26 3.77
1691 4706 4.287067 AGTCCTGTGTTGGTCAGTATCATT 59.713 41.667 0.00 0.00 0.00 2.57
1713 4728 1.728179 CGCGCGTTCATCGGTCTATAT 60.728 52.381 24.19 0.00 40.26 0.86
1722 4739 4.610945 TCATCGGTCTATATGCATATGCG 58.389 43.478 26.21 17.43 45.83 4.73
1752 4769 6.699575 ATCTTTGTTTAGTGTGCAGTTTCT 57.300 33.333 0.00 0.00 0.00 2.52
1754 4771 7.801716 TCTTTGTTTAGTGTGCAGTTTCTAT 57.198 32.000 0.00 0.00 0.00 1.98
1755 4772 8.220755 TCTTTGTTTAGTGTGCAGTTTCTATT 57.779 30.769 0.00 0.00 0.00 1.73
1756 4773 8.682710 TCTTTGTTTAGTGTGCAGTTTCTATTT 58.317 29.630 0.00 0.00 0.00 1.40
1884 4909 3.225235 GGCAGAGAGGCAGGTAGG 58.775 66.667 0.00 0.00 43.51 3.18
1894 4919 3.105283 GAGGCAGGTAGGGTTCTTTCTA 58.895 50.000 0.00 0.00 0.00 2.10
1905 4930 7.126268 GGTAGGGTTCTTTCTATAGGTTACCAA 59.874 40.741 3.51 0.00 0.00 3.67
1961 4989 3.995199 ACATAGACGAATAGGCCATGTG 58.005 45.455 5.01 0.00 0.00 3.21
2153 5181 0.909623 GTACCCACTGGCCACTGTAT 59.090 55.000 0.00 0.00 33.59 2.29
2154 5182 2.112998 GTACCCACTGGCCACTGTATA 58.887 52.381 0.00 0.00 33.59 1.47
2156 5184 1.280998 ACCCACTGGCCACTGTATAAC 59.719 52.381 0.00 0.00 33.59 1.89
2157 5185 1.280710 CCCACTGGCCACTGTATAACA 59.719 52.381 0.00 0.00 0.00 2.41
2158 5186 2.290641 CCCACTGGCCACTGTATAACAA 60.291 50.000 0.00 0.00 0.00 2.83
2159 5187 3.417101 CCACTGGCCACTGTATAACAAA 58.583 45.455 0.00 0.00 0.00 2.83
2160 5188 3.823873 CCACTGGCCACTGTATAACAAAA 59.176 43.478 0.00 0.00 0.00 2.44
2214 5242 4.833478 ATGTGACAAGCTATGAGAAGGT 57.167 40.909 0.00 0.00 0.00 3.50
2252 5280 6.620877 ATCCTAGAACAGTCACAACCATAA 57.379 37.500 0.00 0.00 0.00 1.90
2301 5329 7.096884 ACTAAACAGAGTAATCACGCTCATA 57.903 36.000 0.00 0.00 31.76 2.15
2302 5330 7.717568 ACTAAACAGAGTAATCACGCTCATAT 58.282 34.615 0.00 0.00 31.76 1.78
2303 5331 7.863375 ACTAAACAGAGTAATCACGCTCATATC 59.137 37.037 0.00 0.00 31.76 1.63
2304 5332 5.774498 ACAGAGTAATCACGCTCATATCA 57.226 39.130 0.00 0.00 31.76 2.15
2305 5333 5.767269 ACAGAGTAATCACGCTCATATCAG 58.233 41.667 0.00 0.00 31.76 2.90
2306 5334 5.532779 ACAGAGTAATCACGCTCATATCAGA 59.467 40.000 0.00 0.00 31.76 3.27
2307 5335 6.208402 ACAGAGTAATCACGCTCATATCAGAT 59.792 38.462 0.00 0.00 31.76 2.90
2308 5336 6.746822 CAGAGTAATCACGCTCATATCAGATC 59.253 42.308 0.00 0.00 31.76 2.75
2309 5337 6.432472 AGAGTAATCACGCTCATATCAGATCA 59.568 38.462 0.00 0.00 34.39 2.92
2310 5338 6.385843 AGTAATCACGCTCATATCAGATCAC 58.614 40.000 0.00 0.00 0.00 3.06
2311 5339 4.861102 ATCACGCTCATATCAGATCACA 57.139 40.909 0.00 0.00 0.00 3.58
2312 5340 4.861102 TCACGCTCATATCAGATCACAT 57.139 40.909 0.00 0.00 0.00 3.21
2313 5341 4.802999 TCACGCTCATATCAGATCACATC 58.197 43.478 0.00 0.00 0.00 3.06
2314 5342 4.522022 TCACGCTCATATCAGATCACATCT 59.478 41.667 0.00 0.00 41.15 2.90
2315 5343 5.707298 TCACGCTCATATCAGATCACATCTA 59.293 40.000 0.00 0.00 37.58 1.98
2318 5346 5.804473 CGCTCATATCAGATCACATCTAACC 59.196 44.000 0.00 0.00 37.58 2.85
2323 5351 8.146412 TCATATCAGATCACATCTAACCAGTTG 58.854 37.037 0.00 0.00 37.58 3.16
2331 5359 3.262420 CATCTAACCAGTTGTTCTCCCG 58.738 50.000 0.00 0.00 38.42 5.14
2343 5371 0.179040 TTCTCCCGAAACCGCACTTT 60.179 50.000 0.00 0.00 0.00 2.66
2357 5385 3.548587 CGCACTTTTGTCTCACTTCATG 58.451 45.455 0.00 0.00 0.00 3.07
2384 5415 5.414454 TGAAAACACCCATATTCGAGAAAGG 59.586 40.000 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
236 237 0.032267 GTAGCTGCCGTAGTGATCCC 59.968 60.000 0.00 0.00 0.00 3.85
330 331 2.279784 GCCGGGAAGCTCTCGATG 60.280 66.667 2.18 0.00 44.60 3.84
454 462 2.049156 TGGTCTCTGAACGCGCAG 60.049 61.111 5.73 6.73 37.24 5.18
457 465 1.656095 GAATTCTGGTCTCTGAACGCG 59.344 52.381 3.53 3.53 34.46 6.01
483 491 8.569641 GGACCAAGTACTTCTCTACATATACTG 58.430 40.741 4.77 0.00 0.00 2.74
484 492 7.444792 CGGACCAAGTACTTCTCTACATATACT 59.555 40.741 4.77 0.00 0.00 2.12
485 493 7.308469 CCGGACCAAGTACTTCTCTACATATAC 60.308 44.444 4.77 0.00 0.00 1.47
486 494 6.713903 CCGGACCAAGTACTTCTCTACATATA 59.286 42.308 4.77 0.00 0.00 0.86
487 495 5.535406 CCGGACCAAGTACTTCTCTACATAT 59.465 44.000 4.77 0.00 0.00 1.78
491 507 2.159268 GCCGGACCAAGTACTTCTCTAC 60.159 54.545 5.05 0.00 0.00 2.59
498 514 0.605589 GCAAAGCCGGACCAAGTACT 60.606 55.000 5.05 0.00 0.00 2.73
505 521 1.657751 GAATCCAGCAAAGCCGGACC 61.658 60.000 5.05 0.00 0.00 4.46
512 528 2.229784 GGTTCACCTGAATCCAGCAAAG 59.770 50.000 0.00 0.00 39.07 2.77
515 531 0.770499 TGGTTCACCTGAATCCAGCA 59.230 50.000 0.00 0.00 39.07 4.41
643 3580 3.552699 GTGTTATACAATGCGTCGCCTAA 59.447 43.478 15.88 0.00 0.00 2.69
648 3585 3.982127 TGTGTGTTATACAATGCGTCG 57.018 42.857 0.00 0.00 41.89 5.12
651 3588 8.001358 TCAAAATTTGTGTGTTATACAATGCG 57.999 30.769 5.56 0.00 41.89 4.73
661 3598 9.097257 CCTTCTGTAATTCAAAATTTGTGTGTT 57.903 29.630 5.56 0.50 0.00 3.32
671 3608 5.898120 TGGGATCCCTTCTGTAATTCAAAA 58.102 37.500 31.05 2.00 36.94 2.44
677 3614 5.911178 TCTGTAATGGGATCCCTTCTGTAAT 59.089 40.000 31.05 11.94 36.94 1.89
678 3615 5.285401 TCTGTAATGGGATCCCTTCTGTAA 58.715 41.667 31.05 9.90 36.94 2.41
679 3616 4.890988 TCTGTAATGGGATCCCTTCTGTA 58.109 43.478 31.05 10.70 36.94 2.74
680 3617 3.736094 TCTGTAATGGGATCCCTTCTGT 58.264 45.455 31.05 12.91 36.94 3.41
681 3618 4.778213 TTCTGTAATGGGATCCCTTCTG 57.222 45.455 31.05 19.52 36.94 3.02
682 3619 4.540099 TGTTTCTGTAATGGGATCCCTTCT 59.460 41.667 31.05 17.26 36.94 2.85
683 3620 4.855340 TGTTTCTGTAATGGGATCCCTTC 58.145 43.478 31.05 17.76 36.94 3.46
684 3621 4.946160 TGTTTCTGTAATGGGATCCCTT 57.054 40.909 31.05 22.58 36.94 3.95
685 3622 6.069088 TGTTATGTTTCTGTAATGGGATCCCT 60.069 38.462 31.05 15.06 36.94 4.20
686 3623 6.126409 TGTTATGTTTCTGTAATGGGATCCC 58.874 40.000 25.22 25.22 0.00 3.85
687 3624 7.339466 ACTTGTTATGTTTCTGTAATGGGATCC 59.661 37.037 1.92 1.92 0.00 3.36
688 3625 8.184192 CACTTGTTATGTTTCTGTAATGGGATC 58.816 37.037 0.00 0.00 0.00 3.36
689 3626 7.362920 GCACTTGTTATGTTTCTGTAATGGGAT 60.363 37.037 0.00 0.00 0.00 3.85
690 3627 6.072175 GCACTTGTTATGTTTCTGTAATGGGA 60.072 38.462 0.00 0.00 0.00 4.37
691 3628 6.071952 AGCACTTGTTATGTTTCTGTAATGGG 60.072 38.462 0.00 0.00 0.00 4.00
692 3629 6.913170 AGCACTTGTTATGTTTCTGTAATGG 58.087 36.000 0.00 0.00 0.00 3.16
693 3630 8.075574 TGAAGCACTTGTTATGTTTCTGTAATG 58.924 33.333 3.76 0.00 37.93 1.90
700 3637 5.570589 GCAGATGAAGCACTTGTTATGTTTC 59.429 40.000 0.00 0.00 37.68 2.78
704 3641 4.690184 TGCAGATGAAGCACTTGTTATG 57.310 40.909 0.00 0.00 37.02 1.90
727 3664 2.099141 TTCTCTGTGAAGATTGGGCG 57.901 50.000 0.00 0.00 0.00 6.13
729 3666 6.376299 TCATTGATTTCTCTGTGAAGATTGGG 59.624 38.462 0.00 0.00 35.89 4.12
759 3696 3.262448 TAACCCGGCCCTGCAAGTC 62.262 63.158 0.00 0.00 0.00 3.01
760 3697 3.253838 TAACCCGGCCCTGCAAGT 61.254 61.111 0.00 0.00 0.00 3.16
761 3698 2.438434 CTAACCCGGCCCTGCAAG 60.438 66.667 0.00 0.00 0.00 4.01
764 3701 3.476419 TAGCTAACCCGGCCCTGC 61.476 66.667 0.00 0.00 0.00 4.85
765 3702 2.504519 GTAGCTAACCCGGCCCTG 59.495 66.667 0.00 0.00 0.00 4.45
766 3703 2.767073 GGTAGCTAACCCGGCCCT 60.767 66.667 0.00 0.00 43.16 5.19
767 3704 4.231439 CGGTAGCTAACCCGGCCC 62.231 72.222 13.60 0.09 46.62 5.80
768 3705 2.639883 CTTCGGTAGCTAACCCGGCC 62.640 65.000 19.40 4.60 46.62 6.13
769 3706 1.227176 CTTCGGTAGCTAACCCGGC 60.227 63.158 19.40 0.00 46.62 6.13
770 3707 0.384669 CTCTTCGGTAGCTAACCCGG 59.615 60.000 19.40 7.57 46.62 5.73
771 3708 1.386533 TCTCTTCGGTAGCTAACCCG 58.613 55.000 14.93 14.93 46.62 5.28
772 3709 2.159128 GGTTCTCTTCGGTAGCTAACCC 60.159 54.545 2.43 0.00 46.62 4.11
773 3710 2.759535 AGGTTCTCTTCGGTAGCTAACC 59.240 50.000 2.43 2.02 45.77 2.85
774 3711 4.422840 GAAGGTTCTCTTCGGTAGCTAAC 58.577 47.826 0.00 0.00 41.95 2.34
775 3712 4.715527 GAAGGTTCTCTTCGGTAGCTAA 57.284 45.455 0.00 0.00 41.95 3.09
785 3722 3.835395 ACTCGGATTCTGAAGGTTCTCTT 59.165 43.478 0.00 0.00 38.65 2.85
786 3723 3.436243 ACTCGGATTCTGAAGGTTCTCT 58.564 45.455 0.00 0.00 0.00 3.10
787 3724 3.878160 ACTCGGATTCTGAAGGTTCTC 57.122 47.619 0.00 0.00 0.00 2.87
788 3725 3.128938 CGTACTCGGATTCTGAAGGTTCT 59.871 47.826 0.00 0.00 0.00 3.01
789 3726 3.119566 ACGTACTCGGATTCTGAAGGTTC 60.120 47.826 0.00 0.00 41.85 3.62
790 3727 2.824341 ACGTACTCGGATTCTGAAGGTT 59.176 45.455 0.00 0.00 41.85 3.50
791 3728 2.422832 GACGTACTCGGATTCTGAAGGT 59.577 50.000 0.00 0.00 41.85 3.50
792 3729 2.223525 GGACGTACTCGGATTCTGAAGG 60.224 54.545 0.00 0.00 41.85 3.46
793 3730 2.223525 GGGACGTACTCGGATTCTGAAG 60.224 54.545 0.00 0.00 41.85 3.02
794 3731 1.747355 GGGACGTACTCGGATTCTGAA 59.253 52.381 0.00 0.00 41.85 3.02
795 3732 1.386533 GGGACGTACTCGGATTCTGA 58.613 55.000 0.00 0.00 41.85 3.27
796 3733 3.940723 GGGACGTACTCGGATTCTG 57.059 57.895 0.00 0.00 41.85 3.02
815 3752 1.227002 GATTCTGGAGACGGCCGAC 60.227 63.158 35.90 27.70 36.33 4.79
816 3753 2.423898 GGATTCTGGAGACGGCCGA 61.424 63.158 35.90 7.96 36.33 5.54
817 3754 2.107141 GGATTCTGGAGACGGCCG 59.893 66.667 26.86 26.86 36.33 6.13
818 3755 2.107141 CGGATTCTGGAGACGGCC 59.893 66.667 0.00 0.00 36.33 6.13
837 3774 4.387862 CGGGGAAACGCATACTATACAATC 59.612 45.833 0.00 0.00 45.02 2.67
839 3776 3.493002 CCGGGGAAACGCATACTATACAA 60.493 47.826 0.00 0.00 45.02 2.41
840 3777 2.036217 CCGGGGAAACGCATACTATACA 59.964 50.000 0.00 0.00 45.02 2.29
841 3778 2.680577 CCGGGGAAACGCATACTATAC 58.319 52.381 0.00 0.00 45.02 1.47
842 3779 1.001181 GCCGGGGAAACGCATACTATA 59.999 52.381 2.18 0.00 45.02 1.31
843 3780 0.250166 GCCGGGGAAACGCATACTAT 60.250 55.000 2.18 0.00 45.02 2.12
844 3781 1.144496 GCCGGGGAAACGCATACTA 59.856 57.895 2.18 0.00 45.02 1.82
845 3782 2.124860 GCCGGGGAAACGCATACT 60.125 61.111 2.18 0.00 45.02 2.12
886 3823 8.375506 AGTTTTTCTTTTTCTTTCTTGACCCTT 58.624 29.630 0.00 0.00 0.00 3.95
1043 3991 5.849510 TGGACTCGAAGTAGTTGATGAAAA 58.150 37.500 0.00 0.00 0.00 2.29
1071 4019 4.175489 CTCGACGACGACGGCCAT 62.175 66.667 18.73 0.00 45.81 4.40
1078 4026 3.744719 CAAGGGGCTCGACGACGA 61.745 66.667 9.98 9.98 46.56 4.20
1079 4027 4.796231 CCAAGGGGCTCGACGACG 62.796 72.222 0.00 0.00 41.26 5.12
1277 4243 3.138625 CTCCCACGCATACCCGAT 58.861 61.111 0.00 0.00 0.00 4.18
1288 4257 2.185310 AATCCGACAGGTGCTCCCAC 62.185 60.000 0.00 0.00 41.32 4.61
1327 4296 5.237815 CAGTGTGGTAGAAACTAGCATCAA 58.762 41.667 12.53 1.93 0.00 2.57
1333 4302 4.258702 ACAGCAGTGTGGTAGAAACTAG 57.741 45.455 0.00 0.00 34.75 2.57
1340 4309 2.094494 CAGAGGTACAGCAGTGTGGTAG 60.094 54.545 0.00 0.00 37.52 3.18
1364 4333 6.619801 AAACTTTACCGATCCATAATCTGC 57.380 37.500 0.00 0.00 31.68 4.26
1400 4369 4.781775 TGAAACCACCAAAGAGAACCTA 57.218 40.909 0.00 0.00 0.00 3.08
1401 4370 3.662759 TGAAACCACCAAAGAGAACCT 57.337 42.857 0.00 0.00 0.00 3.50
1403 4372 4.099419 ACCATTGAAACCACCAAAGAGAAC 59.901 41.667 0.00 0.00 0.00 3.01
1405 4374 3.636300 CACCATTGAAACCACCAAAGAGA 59.364 43.478 0.00 0.00 0.00 3.10
1406 4375 3.636300 TCACCATTGAAACCACCAAAGAG 59.364 43.478 0.00 0.00 0.00 2.85
1407 4376 3.636300 CTCACCATTGAAACCACCAAAGA 59.364 43.478 0.00 0.00 0.00 2.52
1426 4395 6.942532 AAAACACAAGCTTAATCTCACTCA 57.057 33.333 0.00 0.00 0.00 3.41
1433 4402 7.928908 TCATCACAAAAACACAAGCTTAATC 57.071 32.000 0.00 0.00 0.00 1.75
1450 4419 7.410120 ACTGTCTACTTACATCATCATCACA 57.590 36.000 0.00 0.00 0.00 3.58
1493 4462 2.492484 ACATAAGTCACAGACCCTCGTC 59.508 50.000 0.00 0.00 39.50 4.20
1527 4497 6.962678 TGTGCGAAAGACAAACTAAAAACTAC 59.037 34.615 0.00 0.00 0.00 2.73
1528 4498 7.074507 TGTGCGAAAGACAAACTAAAAACTA 57.925 32.000 0.00 0.00 0.00 2.24
1529 4499 5.945155 TGTGCGAAAGACAAACTAAAAACT 58.055 33.333 0.00 0.00 0.00 2.66
1530 4500 6.252655 ACATGTGCGAAAGACAAACTAAAAAC 59.747 34.615 0.00 0.00 0.00 2.43
1547 4517 3.627123 TCTCCAATGGATTAACATGTGCG 59.373 43.478 0.87 0.00 0.00 5.34
1639 4650 2.159435 GGCATAAATTTGACGGCGAGTT 60.159 45.455 16.62 0.00 0.00 3.01
1641 4652 1.670811 AGGCATAAATTTGACGGCGAG 59.329 47.619 16.62 0.00 0.00 5.03
1659 4670 0.620556 AACACAGGACTGGCCATAGG 59.379 55.000 5.51 0.00 40.02 2.57
1676 4691 1.267532 CGCGCAATGATACTGACCAAC 60.268 52.381 8.75 0.00 0.00 3.77
1680 4695 1.084037 CGCGCGCAATGATACTGAC 60.084 57.895 32.61 0.00 0.00 3.51
1713 4728 3.407424 AAGATAGAAGGCGCATATGCA 57.593 42.857 26.52 6.30 42.21 3.96
1722 4739 5.181245 TGCACACTAAACAAAGATAGAAGGC 59.819 40.000 0.00 0.00 0.00 4.35
1770 4788 0.375106 GGCTACAAGTCGCATGCTTC 59.625 55.000 17.13 8.46 0.00 3.86
1821 4839 8.936864 GTGTTCAAAGCTATGAAACATAGTAGT 58.063 33.333 16.58 3.76 40.76 2.73
1822 4840 8.935844 TGTGTTCAAAGCTATGAAACATAGTAG 58.064 33.333 16.58 7.59 40.76 2.57
1823 4841 8.840833 TGTGTTCAAAGCTATGAAACATAGTA 57.159 30.769 16.58 0.77 40.76 1.82
1824 4842 7.744087 TGTGTTCAAAGCTATGAAACATAGT 57.256 32.000 16.58 5.00 40.76 2.12
1825 4843 8.506437 TCTTGTGTTCAAAGCTATGAAACATAG 58.494 33.333 12.63 12.63 40.76 2.23
1884 4909 7.769507 CCTCTTTGGTAACCTATAGAAAGAACC 59.230 40.741 0.00 2.50 31.04 3.62
1894 4919 7.691993 ACATGTATCCTCTTTGGTAACCTAT 57.308 36.000 0.00 0.00 37.07 2.57
1905 4930 8.543774 AGAAGACATTTGTACATGTATCCTCTT 58.456 33.333 9.18 9.23 37.52 2.85
1961 4989 1.230324 GATGCTTGATTCGTAGCCCC 58.770 55.000 7.79 0.00 36.56 5.80
2294 5322 5.804473 GGTTAGATGTGATCTGATATGAGCG 59.196 44.000 0.00 0.00 40.51 5.03
2301 5329 6.305272 ACAACTGGTTAGATGTGATCTGAT 57.695 37.500 0.00 0.00 38.36 2.90
2302 5330 5.745312 ACAACTGGTTAGATGTGATCTGA 57.255 39.130 0.00 0.00 38.36 3.27
2303 5331 6.169094 AGAACAACTGGTTAGATGTGATCTG 58.831 40.000 0.00 0.00 38.78 2.90
2304 5332 6.365970 AGAACAACTGGTTAGATGTGATCT 57.634 37.500 0.00 0.00 38.78 2.75
2305 5333 5.582665 GGAGAACAACTGGTTAGATGTGATC 59.417 44.000 0.00 0.00 38.78 2.92
2306 5334 5.491982 GGAGAACAACTGGTTAGATGTGAT 58.508 41.667 0.00 0.00 38.78 3.06
2307 5335 4.262894 GGGAGAACAACTGGTTAGATGTGA 60.263 45.833 0.00 0.00 38.78 3.58
2308 5336 4.003648 GGGAGAACAACTGGTTAGATGTG 58.996 47.826 0.00 0.00 38.78 3.21
2309 5337 3.306780 CGGGAGAACAACTGGTTAGATGT 60.307 47.826 0.00 0.00 41.12 3.06
2310 5338 3.056107 TCGGGAGAACAACTGGTTAGATG 60.056 47.826 0.00 0.00 40.63 2.90
2311 5339 3.170717 TCGGGAGAACAACTGGTTAGAT 58.829 45.455 0.00 0.00 40.63 1.98
2312 5340 2.600790 TCGGGAGAACAACTGGTTAGA 58.399 47.619 0.00 0.00 40.63 2.10
2313 5341 3.396260 TTCGGGAGAACAACTGGTTAG 57.604 47.619 0.00 0.00 45.39 2.34
2331 5359 2.354821 AGTGAGACAAAAGTGCGGTTTC 59.645 45.455 0.00 0.00 0.00 2.78
2343 5371 6.918626 TGTTTTCAAACATGAAGTGAGACAA 58.081 32.000 0.00 0.00 43.45 3.18
2357 5385 6.249035 TCTCGAATATGGGTGTTTTCAAAC 57.751 37.500 0.00 0.00 39.33 2.93


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

AutoCloner maintained by Alex Coulton.