Multiple sequence alignment - TraesCS4D01G281800

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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 TraesCS4D01G281800 chr4D 100.000 4759 0 0 1 4759 453042117 453046875 0.000000e+00 8789.0
1 TraesCS4D01G281800 chr4B 89.140 2744 149 56 2110 4759 566231351 566234039 0.000000e+00 3278.0
2 TraesCS4D01G281800 chr4B 88.928 1418 69 29 745 2107 566228947 566230331 0.000000e+00 1668.0
3 TraesCS4D01G281800 chr4B 89.804 716 40 13 1 708 566228254 566228944 0.000000e+00 887.0
4 TraesCS4D01G281800 chr4A 94.463 1192 46 9 744 1924 14177466 14176284 0.000000e+00 1818.0
5 TraesCS4D01G281800 chr4A 89.950 1403 90 21 2608 3969 14175712 14174320 0.000000e+00 1762.0
6 TraesCS4D01G281800 chr4A 88.112 572 57 6 1964 2527 14176277 14175709 0.000000e+00 669.0
7 TraesCS4D01G281800 chr4A 82.561 734 78 30 1 717 14178160 14177460 6.810000e-168 601.0
8 TraesCS4D01G281800 chr4A 83.009 565 46 29 4220 4759 14170094 14169555 2.590000e-127 466.0
9 TraesCS4D01G281800 chr4A 80.120 166 10 8 4070 4223 14170738 14170584 8.430000e-18 102.0
10 TraesCS4D01G281800 chr4A 80.120 166 10 8 4070 4223 14171397 14171243 8.430000e-18 102.0
11 TraesCS4D01G281800 chr3D 85.526 152 14 7 4211 4360 19208329 19208184 8.250000e-33 152.0
12 TraesCS4D01G281800 chr3D 83.582 67 9 1 445 511 365177187 365177123 1.430000e-05 62.1
13 TraesCS4D01G281800 chr7B 96.552 87 3 0 2526 2612 462733994 462734080 1.380000e-30 145.0
14 TraesCS4D01G281800 chr7B 83.871 124 19 1 3575 3697 741638330 741638453 3.010000e-22 117.0
15 TraesCS4D01G281800 chr7D 93.548 93 5 1 2520 2612 121937437 121937346 2.310000e-28 137.0
16 TraesCS4D01G281800 chr7D 93.103 87 6 0 2525 2611 446245091 446245005 1.390000e-25 128.0
17 TraesCS4D01G281800 chr7D 91.860 86 7 0 2526 2611 151326529 151326444 2.330000e-23 121.0
18 TraesCS4D01G281800 chr7D 85.321 109 14 2 3567 3674 583551864 583551757 1.400000e-20 111.0
19 TraesCS4D01G281800 chr7D 97.727 44 1 0 3142 3185 634756589 634756632 5.110000e-10 76.8
20 TraesCS4D01G281800 chr7A 76.703 279 44 11 2927 3187 731575172 731575447 8.310000e-28 135.0
21 TraesCS4D01G281800 chr7A 81.818 154 27 1 3522 3674 675028021 675027868 1.390000e-25 128.0
22 TraesCS4D01G281800 chr7A 84.127 126 18 1 3545 3670 731673572 731673695 2.330000e-23 121.0
23 TraesCS4D01G281800 chr7A 78.889 180 34 4 3498 3674 675025005 675024827 8.370000e-23 119.0
24 TraesCS4D01G281800 chr1B 94.253 87 5 0 2526 2612 618697664 618697578 2.990000e-27 134.0
25 TraesCS4D01G281800 chr1A 93.407 91 3 3 2522 2611 473033848 473033760 1.070000e-26 132.0
26 TraesCS4D01G281800 chr1A 87.879 99 10 2 2520 2618 36568614 36568518 1.080000e-21 115.0
27 TraesCS4D01G281800 chr3B 91.954 87 7 0 2525 2611 526809081 526808995 6.470000e-24 122.0
28 TraesCS4D01G281800 chrUn 80.120 166 10 8 4070 4223 476625242 476625088 8.430000e-18 102.0
29 TraesCS4D01G281800 chr2B 80.952 105 16 4 1691 1794 12845973 12845872 3.950000e-11 80.5
30 TraesCS4D01G281800 chr6D 97.143 35 0 1 561 594 10214232 10214198 1.850000e-04 58.4
31 TraesCS4D01G281800 chr5A 100.000 29 0 0 561 589 315855600 315855572 2.000000e-03 54.7


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 TraesCS4D01G281800 chr4D 453042117 453046875 4758 False 8789.000000 8789 100.000000 1 4759 1 chr4D.!!$F1 4758
1 TraesCS4D01G281800 chr4B 566228254 566234039 5785 False 1944.333333 3278 89.290667 1 4759 3 chr4B.!!$F1 4758
2 TraesCS4D01G281800 chr4A 14169555 14178160 8605 True 788.571429 1818 85.476429 1 4759 7 chr4A.!!$R1 4758

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
949 990 0.168128 GCAACAAATCGTTCTCCCCG 59.832 55.0 0.0 0.0 34.86 5.73 F
2383 3483 0.244450 CGCTGCCACCACAAATTCAT 59.756 50.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2815 3924 0.392863 TGACATGATGGAAGCACCCG 60.393 55.0 0.00 0.0 30.93 5.28 R
4296 9440 0.034337 TGGTAAACCTCACGGCACTC 59.966 55.0 0.02 0.0 36.82 3.51 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
366 373 1.864711 TCAACCTTTCTTGACTTCGCG 59.135 47.619 0.00 0.00 0.00 5.87
369 377 2.767505 ACCTTTCTTGACTTCGCGAAT 58.232 42.857 23.67 12.59 0.00 3.34
478 493 8.586570 TTGTGAACTTTATTCAAATTCGCAAT 57.413 26.923 7.06 0.00 42.02 3.56
479 494 8.586570 TGTGAACTTTATTCAAATTCGCAATT 57.413 26.923 0.00 0.00 36.98 2.32
480 495 9.039870 TGTGAACTTTATTCAAATTCGCAATTT 57.960 25.926 0.00 2.29 41.57 1.82
481 496 9.862585 GTGAACTTTATTCAAATTCGCAATTTT 57.137 25.926 4.70 0.00 38.97 1.82
484 499 9.579610 AACTTTATTCAAATTCGCAATTTTTCG 57.420 25.926 4.70 0.00 38.97 3.46
485 500 8.973378 ACTTTATTCAAATTCGCAATTTTTCGA 58.027 25.926 4.70 0.00 38.97 3.71
520 535 8.599624 AGTTCCATGGACTTTTTCATATTCAT 57.400 30.769 15.91 0.00 0.00 2.57
527 542 8.365060 TGGACTTTTTCATATTCATGGACAAT 57.635 30.769 0.00 0.00 32.61 2.71
711 730 4.113617 GGGACCAGCTTTTTCCCC 57.886 61.111 11.67 2.39 43.07 4.81
712 731 1.465172 GGGACCAGCTTTTTCCCCT 59.535 57.895 11.67 0.00 43.07 4.79
713 732 0.702316 GGGACCAGCTTTTTCCCCTA 59.298 55.000 11.67 0.00 43.07 3.53
714 733 1.076513 GGGACCAGCTTTTTCCCCTAA 59.923 52.381 11.67 0.00 43.07 2.69
715 734 2.492010 GGGACCAGCTTTTTCCCCTAAA 60.492 50.000 11.67 0.00 43.07 1.85
716 735 2.561419 GGACCAGCTTTTTCCCCTAAAC 59.439 50.000 0.00 0.00 0.00 2.01
717 736 3.497332 GACCAGCTTTTTCCCCTAAACT 58.503 45.455 0.00 0.00 0.00 2.66
718 737 3.895656 GACCAGCTTTTTCCCCTAAACTT 59.104 43.478 0.00 0.00 0.00 2.66
719 738 4.295201 ACCAGCTTTTTCCCCTAAACTTT 58.705 39.130 0.00 0.00 0.00 2.66
720 739 5.460416 ACCAGCTTTTTCCCCTAAACTTTA 58.540 37.500 0.00 0.00 0.00 1.85
721 740 6.082031 ACCAGCTTTTTCCCCTAAACTTTAT 58.918 36.000 0.00 0.00 0.00 1.40
722 741 6.557253 ACCAGCTTTTTCCCCTAAACTTTATT 59.443 34.615 0.00 0.00 0.00 1.40
723 742 7.071950 ACCAGCTTTTTCCCCTAAACTTTATTT 59.928 33.333 0.00 0.00 0.00 1.40
724 743 7.936847 CCAGCTTTTTCCCCTAAACTTTATTTT 59.063 33.333 0.00 0.00 0.00 1.82
725 744 9.990360 CAGCTTTTTCCCCTAAACTTTATTTTA 57.010 29.630 0.00 0.00 0.00 1.52
727 746 9.991906 GCTTTTTCCCCTAAACTTTATTTTAGT 57.008 29.630 0.00 0.00 37.36 2.24
949 990 0.168128 GCAACAAATCGTTCTCCCCG 59.832 55.000 0.00 0.00 34.86 5.73
991 1032 0.491371 GAGATCCATCTCCTCCCCCT 59.509 60.000 5.37 0.00 45.88 4.79
1110 1151 1.981853 CAACCCCAACCCCAATCCG 60.982 63.158 0.00 0.00 0.00 4.18
1377 1427 2.591715 GTATGCCTGCCGCCGATT 60.592 61.111 0.00 0.00 36.24 3.34
1388 1438 0.393077 CCGCCGATTAACTCCATCCT 59.607 55.000 0.00 0.00 0.00 3.24
1427 1477 3.117888 TCCTTTCTCTGCAGTTCCAGTTT 60.118 43.478 14.67 0.00 34.47 2.66
1474 1524 5.237344 AGAAACTGTAGATGCAAAGTCACAC 59.763 40.000 0.00 0.00 0.00 3.82
1509 1559 6.972328 GCCGATGCTTTCATTTCTTGTTATAA 59.028 34.615 0.00 0.00 31.96 0.98
1604 1654 4.277921 TGCTGCACATGAACAAAGAATGTA 59.722 37.500 0.00 0.00 42.99 2.29
1609 1659 5.514204 GCACATGAACAAAGAATGTAGCATC 59.486 40.000 0.00 0.00 42.99 3.91
1633 1683 2.694065 GCTCACTGCACACTTGTCA 58.306 52.632 0.00 0.00 42.31 3.58
1866 1916 7.429636 TGTTGTTACAGGTAAATTGAGTAGC 57.570 36.000 0.00 0.00 0.00 3.58
1874 1924 5.582665 CAGGTAAATTGAGTAGCCTTCAGAC 59.417 44.000 0.00 0.00 0.00 3.51
1923 1973 5.693769 TTATTAGCTCTGCAGGGTTAAGT 57.306 39.130 24.56 16.03 0.00 2.24
1924 1974 6.801718 TTATTAGCTCTGCAGGGTTAAGTA 57.198 37.500 24.56 13.96 0.00 2.24
1925 1975 5.693769 ATTAGCTCTGCAGGGTTAAGTAA 57.306 39.130 24.56 7.37 0.00 2.24
1926 1976 5.492855 TTAGCTCTGCAGGGTTAAGTAAA 57.507 39.130 17.96 0.00 0.00 2.01
1927 1977 3.944087 AGCTCTGCAGGGTTAAGTAAAG 58.056 45.455 16.66 1.17 0.00 1.85
1985 2035 8.948631 AGTCACCACTAACATATGTTATCTTG 57.051 34.615 24.81 20.45 39.49 3.02
2033 2111 8.511604 AAATCTCAATAATGACTTGGTGTAGG 57.488 34.615 0.00 0.00 0.00 3.18
2068 2151 4.860907 CAGGCAATAGAAAAGCAACACATC 59.139 41.667 0.00 0.00 0.00 3.06
2085 2168 7.698130 GCAACACATCAACATAAGGTTATTCTC 59.302 37.037 0.00 0.00 37.72 2.87
2226 3326 7.232534 TGGCATAAGATTATGTTTATGGGGAAC 59.767 37.037 12.80 0.00 41.92 3.62
2288 3388 1.005450 GGGGTTTCCTTCCATGCTGTA 59.995 52.381 0.00 0.00 0.00 2.74
2319 3419 1.427592 GAGCAGTCTTCCGAGCATGC 61.428 60.000 10.51 10.51 35.53 4.06
2359 3459 4.553330 TTAGCTCCTTCAGGGTTAAGTG 57.447 45.455 0.00 0.00 36.25 3.16
2383 3483 0.244450 CGCTGCCACCACAAATTCAT 59.756 50.000 0.00 0.00 0.00 2.57
2413 3513 2.693210 TCACTATGGGATGATGGCTGA 58.307 47.619 0.00 0.00 0.00 4.26
2510 3610 8.373048 ACACATTGACGTAAAGATCTGTTAAA 57.627 30.769 0.00 0.00 0.00 1.52
2523 3623 7.687941 AGATCTGTTAAACGGACATGAAAAT 57.312 32.000 0.00 0.00 36.13 1.82
2535 3635 3.871594 GACATGAAAATGTACTCCCTCCG 59.128 47.826 0.00 0.00 34.45 4.63
2547 3647 4.405756 ACTCCCTCCGATCCATATTACT 57.594 45.455 0.00 0.00 0.00 2.24
2548 3648 4.753186 ACTCCCTCCGATCCATATTACTT 58.247 43.478 0.00 0.00 0.00 2.24
2549 3649 4.528596 ACTCCCTCCGATCCATATTACTTG 59.471 45.833 0.00 0.00 0.00 3.16
2550 3650 4.489737 TCCCTCCGATCCATATTACTTGT 58.510 43.478 0.00 0.00 0.00 3.16
2551 3651 4.527038 TCCCTCCGATCCATATTACTTGTC 59.473 45.833 0.00 0.00 0.00 3.18
2552 3652 4.486090 CCTCCGATCCATATTACTTGTCG 58.514 47.826 0.00 0.00 0.00 4.35
2589 3689 6.391227 ACTTTGTACTAAAGCTGCAACAAT 57.609 33.333 1.02 0.00 0.00 2.71
2666 3766 4.517285 TCCTTATCATGCCACTTCAGAAC 58.483 43.478 0.00 0.00 0.00 3.01
2669 3769 5.220989 CCTTATCATGCCACTTCAGAACATG 60.221 44.000 5.48 5.48 39.53 3.21
2732 3832 9.367160 CAAGATTATGTTTAGGGGGAATATGTT 57.633 33.333 0.00 0.00 0.00 2.71
2782 3883 8.945481 TTTCACAGATTTCAATTGATTGTGTT 57.055 26.923 25.50 10.89 38.84 3.32
2789 3890 9.683069 AGATTTCAATTGATTGTGTTGTCTAAC 57.317 29.630 9.40 0.00 38.84 2.34
2835 3944 1.386533 GGGTGCTTCCATCATGTCAG 58.613 55.000 0.00 0.00 38.11 3.51
2837 3946 2.440409 GGTGCTTCCATCATGTCAGTT 58.560 47.619 0.00 0.00 35.97 3.16
2880 3989 3.319137 TGTATTCCTCACTGACACTGC 57.681 47.619 0.00 0.00 0.00 4.40
3034 4143 7.761704 TGTTTTGTTTAAAGTGCACATACACAT 59.238 29.630 21.04 0.00 43.23 3.21
3039 4148 8.664798 TGTTTAAAGTGCACATACACATATCTC 58.335 33.333 21.04 0.00 43.23 2.75
3047 4158 7.440556 GTGCACATACACATATCTCTGATTCTT 59.559 37.037 13.17 0.00 40.40 2.52
3115 4226 5.316167 TCCAGTAACATCAAATTGCTCACT 58.684 37.500 0.00 0.00 0.00 3.41
3116 4227 6.472016 TCCAGTAACATCAAATTGCTCACTA 58.528 36.000 0.00 0.00 0.00 2.74
3155 4268 3.490348 CACACAAGAAGACCCAATCCTT 58.510 45.455 0.00 0.00 0.00 3.36
3310 4423 6.296026 ACTCTGCCTTGTTTAACTTGACATA 58.704 36.000 0.00 0.00 0.00 2.29
3345 4465 8.414003 CAGCTCTAAGGACACATATGTAAGTTA 58.586 37.037 8.32 3.92 39.95 2.24
3354 4476 7.305820 GGACACATATGTAAGTTACGTGATTCG 60.306 40.741 19.39 8.15 39.95 3.34
3471 4603 6.408035 TGGACTCTGTACTCTAGTTACTCTG 58.592 44.000 0.00 0.00 0.00 3.35
3489 4621 1.480954 CTGGTAGGAGTGTTATGCGGT 59.519 52.381 0.00 0.00 0.00 5.68
3611 4743 3.975312 AGAAGCATCAAGATGGAGAGGAT 59.025 43.478 11.66 0.00 39.16 3.24
3612 4744 3.773418 AGCATCAAGATGGAGAGGATG 57.227 47.619 11.66 0.00 39.16 3.51
3692 4824 0.175760 CTAACAGGCTCAAGGCGCTA 59.824 55.000 7.64 0.00 46.23 4.26
3757 4889 4.381718 GCCTACTACTGAAACTACCACCTG 60.382 50.000 0.00 0.00 0.00 4.00
3791 4923 0.881118 TTTGAATCACTCCGCCTTGC 59.119 50.000 0.00 0.00 0.00 4.01
3797 4929 0.537143 TCACTCCGCCTTGCATGTTT 60.537 50.000 0.00 0.00 0.00 2.83
3798 4930 0.387622 CACTCCGCCTTGCATGTTTG 60.388 55.000 0.00 0.00 0.00 2.93
3800 4932 2.216750 CTCCGCCTTGCATGTTTGGG 62.217 60.000 0.00 0.00 0.00 4.12
3801 4933 2.432972 CGCCTTGCATGTTTGGGC 60.433 61.111 9.82 9.82 39.43 5.36
3814 4949 2.289756 TGTTTGGGCGTGTAAGCATAGA 60.290 45.455 0.00 0.00 39.27 1.98
3826 4961 5.411361 GTGTAAGCATAGATGGTGTGTTTCA 59.589 40.000 0.00 0.00 38.70 2.69
3847 4990 4.819088 TCATGAAGATGGTGTTCGTTGAAA 59.181 37.500 0.00 0.00 0.00 2.69
3861 5004 7.434013 GTGTTCGTTGAAATTGAGGTGTAAAAT 59.566 33.333 0.00 0.00 0.00 1.82
3865 5008 6.920758 CGTTGAAATTGAGGTGTAAAATCCAA 59.079 34.615 0.00 0.00 0.00 3.53
3867 5010 8.764287 GTTGAAATTGAGGTGTAAAATCCAAAG 58.236 33.333 0.00 0.00 0.00 2.77
3871 5014 6.399639 TTGAGGTGTAAAATCCAAAGAACC 57.600 37.500 0.00 0.00 0.00 3.62
3875 5018 7.780745 TGAGGTGTAAAATCCAAAGAACCTTTA 59.219 33.333 0.00 0.00 36.93 1.85
3876 5019 8.721133 AGGTGTAAAATCCAAAGAACCTTTAT 57.279 30.769 0.00 0.00 32.96 1.40
3877 5020 8.585018 AGGTGTAAAATCCAAAGAACCTTTATG 58.415 33.333 0.00 0.00 32.96 1.90
3909 5055 0.877071 AAGCTGGTGATCTGTTTGCG 59.123 50.000 0.00 0.00 0.00 4.85
3925 5071 2.839486 TGCGAGAAGAGTTGGTGAAT 57.161 45.000 0.00 0.00 0.00 2.57
3926 5072 2.416747 TGCGAGAAGAGTTGGTGAATG 58.583 47.619 0.00 0.00 0.00 2.67
3928 5074 2.693069 CGAGAAGAGTTGGTGAATGCT 58.307 47.619 0.00 0.00 0.00 3.79
3932 5078 2.283145 AGAGTTGGTGAATGCTGCTT 57.717 45.000 0.00 0.00 0.00 3.91
3937 5083 5.244626 AGAGTTGGTGAATGCTGCTTTATTT 59.755 36.000 0.00 0.00 0.00 1.40
3950 5096 2.558359 GCTTTATTTCTGTGCTGGTGGT 59.442 45.455 0.00 0.00 0.00 4.16
3954 5100 0.840617 TTTCTGTGCTGGTGGTGGTA 59.159 50.000 0.00 0.00 0.00 3.25
3984 5150 6.655425 AGCTACAGAATTTAGGTGTTTTCTCC 59.345 38.462 0.00 0.00 0.00 3.71
3991 5158 8.150296 AGAATTTAGGTGTTTTCTCCCAATTTG 58.850 33.333 0.00 0.00 32.11 2.32
3996 5163 3.747529 GTGTTTTCTCCCAATTTGCCATG 59.252 43.478 0.00 0.00 0.00 3.66
3997 5164 3.390639 TGTTTTCTCCCAATTTGCCATGT 59.609 39.130 0.00 0.00 0.00 3.21
3998 5165 4.590647 TGTTTTCTCCCAATTTGCCATGTA 59.409 37.500 0.00 0.00 0.00 2.29
3999 5166 5.170748 GTTTTCTCCCAATTTGCCATGTAG 58.829 41.667 0.00 0.00 0.00 2.74
4006 5173 3.573967 CCAATTTGCCATGTAGGTATCCC 59.426 47.826 0.00 0.00 40.61 3.85
4007 5174 2.631160 TTTGCCATGTAGGTATCCCG 57.369 50.000 0.00 0.00 40.61 5.14
4009 5176 0.399376 TGCCATGTAGGTATCCCGGT 60.399 55.000 0.00 0.00 40.61 5.28
4021 5188 3.496160 GGTATCCCGGTGCATCTGTTATT 60.496 47.826 0.00 0.00 0.00 1.40
4027 5194 1.678101 GGTGCATCTGTTATTGCTCCC 59.322 52.381 5.01 0.00 43.40 4.30
4039 5211 0.112995 TTGCTCCCTGATTGCAACCT 59.887 50.000 0.00 0.00 41.06 3.50
4051 5223 1.689984 TGCAACCTTGAGACATGCAA 58.310 45.000 0.00 0.00 43.39 4.08
4053 5225 1.610522 GCAACCTTGAGACATGCAACT 59.389 47.619 0.00 0.00 37.00 3.16
4057 5229 2.040813 ACCTTGAGACATGCAACTGGAT 59.959 45.455 0.00 0.00 0.00 3.41
4059 5231 3.128242 CCTTGAGACATGCAACTGGATTC 59.872 47.826 0.00 0.00 0.00 2.52
4062 5235 5.101648 TGAGACATGCAACTGGATTCATA 57.898 39.130 0.00 0.00 0.00 2.15
4124 8104 6.334989 TGAATGTTGATGAGAATTGGATTGC 58.665 36.000 0.00 0.00 0.00 3.56
4166 8158 4.081406 TCCATCATGAAGAACCTTTGTGG 58.919 43.478 0.00 0.00 42.93 4.17
4167 8159 3.194116 CCATCATGAAGAACCTTTGTGGG 59.806 47.826 0.00 0.00 41.11 4.61
4186 8832 0.179018 GTACATTAGCCCTGCCCTGG 60.179 60.000 0.00 0.00 0.00 4.45
4218 8864 1.069596 CTGCTTTTGGGGCCAACAC 59.930 57.895 4.39 0.00 35.46 3.32
4226 9365 2.519780 GGGCCAACACGTTTCCCA 60.520 61.111 4.39 0.00 34.61 4.37
4296 9440 6.680810 TGAGTAAAGGCAAGTTGAAATCATG 58.319 36.000 7.16 0.00 0.00 3.07
4303 9447 3.495193 CAAGTTGAAATCATGAGTGCCG 58.505 45.455 0.09 0.00 0.00 5.69
4487 9638 2.955660 TCCAATTTCCGTTATCATGGCC 59.044 45.455 0.00 0.00 0.00 5.36
4492 9643 2.253758 CCGTTATCATGGCCTGGCG 61.254 63.158 13.40 0.00 0.00 5.69
4510 9666 2.516930 ATGGCGGGCTCCAAATCG 60.517 61.111 2.38 0.00 39.96 3.34
4542 9698 1.399440 CTCACCAGGAATCATTGCGTG 59.601 52.381 0.00 0.00 0.00 5.34
4554 9710 0.820891 ATTGCGTGATGCCCTCATCC 60.821 55.000 0.00 0.00 46.60 3.51
4592 9752 0.323302 TATGCCAAGTTGCCGACTGA 59.677 50.000 0.00 0.00 39.00 3.41
4616 9778 2.380660 CAATTTGGTCGTGTGGAAACG 58.619 47.619 0.00 0.00 44.92 3.60
4617 9779 0.948678 ATTTGGTCGTGTGGAAACGG 59.051 50.000 0.00 0.00 43.73 4.44
4619 9781 1.090625 TTGGTCGTGTGGAAACGGTG 61.091 55.000 0.00 0.00 43.73 4.94
4620 9782 2.629763 GTCGTGTGGAAACGGTGC 59.370 61.111 0.00 0.00 43.73 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
330 337 5.629079 AGGTTGATGAGAATTCCGAAAAC 57.371 39.130 0.65 1.43 0.00 2.43
437 450 6.044682 AGTTCACAAATTCAAAAAGCTCTGG 58.955 36.000 0.00 0.00 0.00 3.86
520 535 7.169158 AGTTCTCAAAGTTGAAAATTGTCCA 57.831 32.000 0.00 0.00 36.64 4.02
664 681 0.624254 GGGGGAAAACGGGATCTTCT 59.376 55.000 0.00 0.00 0.00 2.85
665 682 0.624254 AGGGGGAAAACGGGATCTTC 59.376 55.000 0.00 0.00 0.00 2.87
690 707 0.112412 GGAAAAAGCTGGTCCCCTCA 59.888 55.000 0.00 0.00 0.00 3.86
723 742 9.519191 GTTTAGGGGGAAAAAGTGTTATACTAA 57.481 33.333 0.00 0.00 39.18 2.24
724 743 7.823799 CGTTTAGGGGGAAAAAGTGTTATACTA 59.176 37.037 0.00 0.00 39.18 1.82
725 744 6.656270 CGTTTAGGGGGAAAAAGTGTTATACT 59.344 38.462 0.00 0.00 42.89 2.12
726 745 6.654582 TCGTTTAGGGGGAAAAAGTGTTATAC 59.345 38.462 0.00 0.00 0.00 1.47
727 746 6.777782 TCGTTTAGGGGGAAAAAGTGTTATA 58.222 36.000 0.00 0.00 0.00 0.98
728 747 5.633117 TCGTTTAGGGGGAAAAAGTGTTAT 58.367 37.500 0.00 0.00 0.00 1.89
729 748 5.046288 TCGTTTAGGGGGAAAAAGTGTTA 57.954 39.130 0.00 0.00 0.00 2.41
730 749 3.887110 CTCGTTTAGGGGGAAAAAGTGTT 59.113 43.478 0.00 0.00 0.00 3.32
731 750 3.483421 CTCGTTTAGGGGGAAAAAGTGT 58.517 45.455 0.00 0.00 0.00 3.55
732 751 2.228103 GCTCGTTTAGGGGGAAAAAGTG 59.772 50.000 0.00 0.00 0.00 3.16
733 752 2.511659 GCTCGTTTAGGGGGAAAAAGT 58.488 47.619 0.00 0.00 0.00 2.66
734 753 1.467342 CGCTCGTTTAGGGGGAAAAAG 59.533 52.381 0.00 0.00 34.82 2.27
735 754 1.072015 TCGCTCGTTTAGGGGGAAAAA 59.928 47.619 0.00 0.00 39.53 1.94
736 755 0.686224 TCGCTCGTTTAGGGGGAAAA 59.314 50.000 0.00 0.00 39.53 2.29
737 756 0.037046 GTCGCTCGTTTAGGGGGAAA 60.037 55.000 0.00 0.00 44.34 3.13
738 757 1.186917 TGTCGCTCGTTTAGGGGGAA 61.187 55.000 0.00 0.00 44.34 3.97
739 758 1.607178 TGTCGCTCGTTTAGGGGGA 60.607 57.895 0.00 0.00 40.26 4.81
740 759 1.447314 GTGTCGCTCGTTTAGGGGG 60.447 63.158 0.00 0.00 38.66 5.40
741 760 1.804326 CGTGTCGCTCGTTTAGGGG 60.804 63.158 0.00 0.00 38.66 4.79
742 761 0.387622 TTCGTGTCGCTCGTTTAGGG 60.388 55.000 2.34 0.00 39.48 3.53
785 804 0.249322 CCGTGCTACGATCCGGATTT 60.249 55.000 20.22 11.53 46.05 2.17
810 829 3.119319 TCCCACTGTTATTGCCTATGGA 58.881 45.455 0.00 0.00 0.00 3.41
949 990 2.289565 GATTTGGGAATCGGAGTGGAC 58.710 52.381 0.00 0.00 32.96 4.02
1014 1055 3.883744 CTTGAAGCAGCCCGTCGGT 62.884 63.158 11.06 0.00 0.00 4.69
1388 1438 4.927267 AAGGAGGTATTCATTGTCCACA 57.073 40.909 0.00 0.00 0.00 4.17
1427 1477 5.623956 ACACGGGGTTGATCATCTAATTA 57.376 39.130 0.00 0.00 0.00 1.40
1633 1683 3.392616 AGGCCAACGGAGATCAGAATAAT 59.607 43.478 5.01 0.00 0.00 1.28
1866 1916 3.771577 ACCCTGTAACTTGTCTGAAGG 57.228 47.619 0.00 0.00 0.00 3.46
1874 1924 5.438761 CTGAAAGGAAACCCTGTAACTTG 57.561 43.478 0.00 0.00 33.44 3.16
1927 1977 2.038557 TCTCCTGCCAAAGTAAGGTGAC 59.961 50.000 0.00 0.00 30.63 3.67
1985 2035 3.571401 ACAAAGCCATCAAGCCATATAGC 59.429 43.478 0.00 0.00 0.00 2.97
1995 2070 9.806203 CATTATTGAGATTTACAAAGCCATCAA 57.194 29.630 0.00 0.00 0.00 2.57
2033 2111 2.939460 ATTGCCTGCCGTCATAAAAC 57.061 45.000 0.00 0.00 0.00 2.43
2068 2151 6.884295 TCACTTGGGAGAATAACCTTATGTTG 59.116 38.462 0.00 0.00 37.83 3.33
2085 2168 7.504924 TGTACTCTTTTTATGTTCACTTGGG 57.495 36.000 0.00 0.00 0.00 4.12
2226 3326 7.207383 TCAAGGATACGGTAATTCTACACATG 58.793 38.462 0.00 0.00 46.39 3.21
2288 3388 5.106555 CGGAAGACTGCTCAATTTACATGTT 60.107 40.000 2.30 0.00 0.00 2.71
2319 3419 7.375106 AGCTAATCAAATCAGTTCAGTTGAG 57.625 36.000 0.00 0.00 34.09 3.02
2383 3483 7.830697 CCATCATCCCATAGTGAAATAGCATAA 59.169 37.037 0.00 0.00 0.00 1.90
2485 3585 7.956420 TTAACAGATCTTTACGTCAATGTGT 57.044 32.000 0.00 0.00 0.00 3.72
2510 3610 3.263425 AGGGAGTACATTTTCATGTCCGT 59.737 43.478 0.00 0.00 43.06 4.69
2523 3623 3.827817 ATATGGATCGGAGGGAGTACA 57.172 47.619 0.00 0.00 0.00 2.90
2535 3635 4.310769 AGCTGCGACAAGTAATATGGATC 58.689 43.478 0.00 0.00 0.00 3.36
2547 3647 3.724374 AGTTGTACTAAAGCTGCGACAA 58.276 40.909 0.00 0.00 0.00 3.18
2548 3648 3.380479 AGTTGTACTAAAGCTGCGACA 57.620 42.857 0.00 0.00 0.00 4.35
2549 3649 4.025145 ACAAAGTTGTACTAAAGCTGCGAC 60.025 41.667 0.00 0.00 40.16 5.19
2550 3650 4.124238 ACAAAGTTGTACTAAAGCTGCGA 58.876 39.130 0.00 0.00 40.16 5.10
2551 3651 4.468095 ACAAAGTTGTACTAAAGCTGCG 57.532 40.909 0.00 0.00 40.16 5.18
2583 3683 9.354673 ACTCCCTCCAATACATATTAATTGTTG 57.645 33.333 0.00 0.00 32.34 3.33
2589 3689 8.994500 TGTTGTACTCCCTCCAATACATATTAA 58.006 33.333 0.00 0.00 0.00 1.40
2600 3700 3.167485 ACGTATTGTTGTACTCCCTCCA 58.833 45.455 0.00 0.00 0.00 3.86
2648 3748 3.628942 GCATGTTCTGAAGTGGCATGATA 59.371 43.478 17.75 0.00 39.21 2.15
2666 3766 3.945921 ACAGATTGATGAGAAGGTGCATG 59.054 43.478 0.00 0.00 0.00 4.06
2669 3769 4.005650 TCAACAGATTGATGAGAAGGTGC 58.994 43.478 0.00 0.00 40.01 5.01
2732 3832 9.959721 AATAGCTCAAGGACAAGTTAAATCTAA 57.040 29.630 0.00 0.00 0.00 2.10
2782 3883 7.661536 AAGAAGTATCTAGCCATGTTAGACA 57.338 36.000 6.39 0.00 33.77 3.41
2793 3894 7.548427 ACCCGAAAACTAAAAGAAGTATCTAGC 59.452 37.037 0.00 0.00 33.77 3.42
2815 3924 0.392863 TGACATGATGGAAGCACCCG 60.393 55.000 0.00 0.00 30.93 5.28
2835 3944 1.420138 TCCAGGGAGAACAAGGTCAAC 59.580 52.381 0.00 0.00 0.00 3.18
2837 3946 1.056660 GTCCAGGGAGAACAAGGTCA 58.943 55.000 0.00 0.00 0.00 4.02
2880 3989 5.815233 TGCATCTCTAAGATAAGGAAGGG 57.185 43.478 0.00 0.00 32.12 3.95
3047 4158 8.478066 AGAGATACATGCAAGTACTTGTAATCA 58.522 33.333 30.90 22.08 42.31 2.57
3053 4164 7.223582 CAGGTTAGAGATACATGCAAGTACTTG 59.776 40.741 27.85 27.85 43.14 3.16
3102 4213 4.761227 TGCAACAGATAGTGAGCAATTTGA 59.239 37.500 0.00 0.00 37.63 2.69
3155 4268 3.787394 GACGGAGGTTCTGTCCCA 58.213 61.111 6.76 0.00 44.85 4.37
3354 4476 7.587037 TCTATTTTCATTTCATGGATGGGAC 57.413 36.000 9.23 0.00 0.00 4.46
3471 4603 2.685850 AACCGCATAACACTCCTACC 57.314 50.000 0.00 0.00 0.00 3.18
3489 4621 7.763172 ACGAAACAATGCATCACTTTTTAAA 57.237 28.000 0.00 0.00 0.00 1.52
3537 4669 1.337635 GCCTCCATCGCCAGATCTTAG 60.338 57.143 0.00 0.00 34.23 2.18
3692 4824 4.146075 GCTGCTGCCGCTCTCTCT 62.146 66.667 8.89 0.00 36.97 3.10
3722 4854 1.035932 TAGTAGGCTGCGACTGGGAC 61.036 60.000 14.08 0.00 0.00 4.46
3757 4889 0.383949 TCAAAACCCTGCACGCTTTC 59.616 50.000 0.00 0.00 0.00 2.62
3791 4923 0.595588 TGCTTACACGCCCAAACATG 59.404 50.000 0.00 0.00 0.00 3.21
3797 4929 1.202639 CCATCTATGCTTACACGCCCA 60.203 52.381 0.00 0.00 0.00 5.36
3798 4930 1.202651 ACCATCTATGCTTACACGCCC 60.203 52.381 0.00 0.00 0.00 6.13
3800 4932 2.285220 CACACCATCTATGCTTACACGC 59.715 50.000 0.00 0.00 0.00 5.34
3801 4933 3.521560 ACACACCATCTATGCTTACACG 58.478 45.455 0.00 0.00 0.00 4.49
3814 4949 4.219070 CACCATCTTCATGAAACACACCAT 59.781 41.667 9.88 0.00 30.57 3.55
3826 4961 5.964958 ATTTCAACGAACACCATCTTCAT 57.035 34.783 0.00 0.00 0.00 2.57
3847 4990 6.782494 AGGTTCTTTGGATTTTACACCTCAAT 59.218 34.615 0.00 0.00 0.00 2.57
3867 5010 5.794894 TCAGACTGGAGAACATAAAGGTTC 58.205 41.667 1.81 0.00 45.87 3.62
3871 5014 5.350914 CAGCTTCAGACTGGAGAACATAAAG 59.649 44.000 15.45 2.93 0.00 1.85
3875 5018 3.331478 CAGCTTCAGACTGGAGAACAT 57.669 47.619 15.45 0.00 0.00 2.71
3876 5019 2.827800 CAGCTTCAGACTGGAGAACA 57.172 50.000 15.45 0.00 0.00 3.18
3884 5027 2.255406 ACAGATCACCAGCTTCAGACT 58.745 47.619 0.00 0.00 0.00 3.24
3886 5029 3.405831 CAAACAGATCACCAGCTTCAGA 58.594 45.455 0.00 0.00 0.00 3.27
3887 5030 2.095364 GCAAACAGATCACCAGCTTCAG 60.095 50.000 0.00 0.00 0.00 3.02
3888 5031 1.881973 GCAAACAGATCACCAGCTTCA 59.118 47.619 0.00 0.00 0.00 3.02
3898 5043 3.124297 CCAACTCTTCTCGCAAACAGATC 59.876 47.826 0.00 0.00 0.00 2.75
3909 5055 2.161211 GCAGCATTCACCAACTCTTCTC 59.839 50.000 0.00 0.00 0.00 2.87
3925 5071 2.229543 CCAGCACAGAAATAAAGCAGCA 59.770 45.455 0.00 0.00 0.00 4.41
3926 5072 2.229784 ACCAGCACAGAAATAAAGCAGC 59.770 45.455 0.00 0.00 0.00 5.25
3928 5074 2.557924 CCACCAGCACAGAAATAAAGCA 59.442 45.455 0.00 0.00 0.00 3.91
3932 5078 2.158534 ACCACCACCAGCACAGAAATAA 60.159 45.455 0.00 0.00 0.00 1.40
3937 5083 0.471022 TCTACCACCACCAGCACAGA 60.471 55.000 0.00 0.00 0.00 3.41
3950 5096 6.212791 ACCTAAATTCTGTAGCTTGTCTACCA 59.787 38.462 0.00 0.00 45.56 3.25
3954 5100 6.115448 ACACCTAAATTCTGTAGCTTGTCT 57.885 37.500 0.00 0.00 0.00 3.41
3966 5112 7.095229 GCAAATTGGGAGAAAACACCTAAATTC 60.095 37.037 0.00 0.00 31.06 2.17
3969 5115 5.454045 GGCAAATTGGGAGAAAACACCTAAA 60.454 40.000 0.00 0.00 31.06 1.85
3970 5116 4.039852 GGCAAATTGGGAGAAAACACCTAA 59.960 41.667 0.00 0.00 0.00 2.69
3974 5140 3.467374 TGGCAAATTGGGAGAAAACAC 57.533 42.857 0.00 0.00 0.00 3.32
3984 5150 4.853924 GGATACCTACATGGCAAATTGG 57.146 45.455 0.00 0.00 40.22 3.16
4006 5173 1.331756 GGAGCAATAACAGATGCACCG 59.668 52.381 0.00 0.00 44.95 4.94
4009 5176 2.239402 TCAGGGAGCAATAACAGATGCA 59.761 45.455 0.00 0.00 44.95 3.96
4021 5188 0.112995 AAGGTTGCAATCAGGGAGCA 59.887 50.000 13.22 0.00 36.32 4.26
4027 5194 3.672511 GCATGTCTCAAGGTTGCAATCAG 60.673 47.826 13.22 4.06 33.58 2.90
4039 5211 3.753815 TGAATCCAGTTGCATGTCTCAA 58.246 40.909 0.00 0.00 0.00 3.02
4080 8059 5.008619 TCAGAGCTTCAGATCTCACATTC 57.991 43.478 0.00 0.00 38.98 2.67
4082 8061 5.104859 ACATTCAGAGCTTCAGATCTCACAT 60.105 40.000 0.00 0.00 38.98 3.21
4083 8062 4.222366 ACATTCAGAGCTTCAGATCTCACA 59.778 41.667 0.00 0.00 38.98 3.58
4084 8063 4.757594 ACATTCAGAGCTTCAGATCTCAC 58.242 43.478 0.00 0.00 38.98 3.51
4090 8069 5.046807 TCTCATCAACATTCAGAGCTTCAGA 60.047 40.000 0.00 0.00 0.00 3.27
4124 8104 4.943093 TGGACACACATGATTCCATACAAG 59.057 41.667 0.00 0.00 33.02 3.16
4166 8158 0.179018 CAGGGCAGGGCTAATGTACC 60.179 60.000 0.00 0.00 0.00 3.34
4167 8159 0.179018 CCAGGGCAGGGCTAATGTAC 60.179 60.000 0.00 0.00 0.00 2.90
4186 8832 3.831715 AAAGCAGGATAGTTTGTTCGC 57.168 42.857 0.00 0.00 0.00 4.70
4238 9377 1.822615 GCTCCTGCCTCCTCTTCTC 59.177 63.158 0.00 0.00 0.00 2.87
4249 9388 1.673665 CAGTTCTGGTGGCTCCTGC 60.674 63.158 7.19 0.00 37.07 4.85
4296 9440 0.034337 TGGTAAACCTCACGGCACTC 59.966 55.000 0.02 0.00 36.82 3.51
4303 9447 7.363530 GGGGAATTTAAGAATGGTAAACCTCAC 60.364 40.741 0.02 0.00 36.82 3.51
4360 9505 1.264826 TGCGCGTAGTATGCTTCGATA 59.735 47.619 13.65 0.00 37.65 2.92
4492 9643 2.546494 CGATTTGGAGCCCGCCATC 61.546 63.158 0.00 0.00 37.86 3.51
4510 9666 2.099263 TCCTGGTGAGTTCGATTCGATC 59.901 50.000 9.96 9.26 35.23 3.69
4519 9675 2.096496 CGCAATGATTCCTGGTGAGTTC 59.904 50.000 0.00 0.00 0.00 3.01
4554 9710 0.683504 AGTGGTGCTACCTAGGACGG 60.684 60.000 17.98 5.91 44.42 4.79
4592 9752 0.667993 CCACACGACCAAATTGCAGT 59.332 50.000 0.00 0.00 0.00 4.40
4616 9778 1.648467 GGCTCGATTTGGTCAGCACC 61.648 60.000 0.00 0.00 44.10 5.01
4617 9779 1.796796 GGCTCGATTTGGTCAGCAC 59.203 57.895 0.00 0.00 34.62 4.40
4619 9781 2.464459 CCGGCTCGATTTGGTCAGC 61.464 63.158 0.00 0.00 33.18 4.26
4620 9782 2.464459 GCCGGCTCGATTTGGTCAG 61.464 63.158 22.15 0.00 0.00 3.51
4647 9817 0.179048 TTCGACGTAGCTATCCGGGA 60.179 55.000 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.