Multiple sequence alignment - TraesCS7D01G199100

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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 TraesCS7D01G199100 chr7D 100.000 5657 0 0 437 6093 156214374 156220030 0.000000e+00 10447.0
1 TraesCS7D01G199100 chr7D 100.000 235 0 0 1 235 156213938 156214172 9.380000e-118 435.0
2 TraesCS7D01G199100 chr7D 92.857 266 18 1 5498 5763 351294251 351294515 9.580000e-103 385.0
3 TraesCS7D01G199100 chr7D 90.877 285 14 6 4967 5250 351293464 351293737 7.460000e-99 372.0
4 TraesCS7D01G199100 chr7D 88.991 109 8 2 5255 5363 351293810 351293914 1.380000e-26 132.0
5 TraesCS7D01G199100 chr7D 98.000 50 1 0 4571 4620 156218457 156218506 3.030000e-13 87.9
6 TraesCS7D01G199100 chr7D 98.000 50 1 0 4520 4569 156218508 156218557 3.030000e-13 87.9
7 TraesCS7D01G199100 chr7A 91.333 2769 126 46 437 3159 210849862 210852562 0.000000e+00 3679.0
8 TraesCS7D01G199100 chr7A 95.783 1494 46 11 3149 4626 210852961 210854453 0.000000e+00 2394.0
9 TraesCS7D01G199100 chr7A 88.785 749 54 18 4521 5250 210854399 210855136 0.000000e+00 891.0
10 TraesCS7D01G199100 chr7A 92.013 601 44 2 5495 6093 210855723 210856321 0.000000e+00 841.0
11 TraesCS7D01G199100 chr7A 91.026 234 19 2 3 235 210849575 210849807 1.270000e-81 315.0
12 TraesCS7D01G199100 chr7A 93.182 44 2 1 3795 3838 579340238 579340280 5.100000e-06 63.9
13 TraesCS7D01G199100 chr7B 91.242 2569 126 36 924 3439 118642068 118644590 0.000000e+00 3406.0
14 TraesCS7D01G199100 chr7B 95.781 640 21 3 3993 4626 118645247 118645886 0.000000e+00 1027.0
15 TraesCS7D01G199100 chr7B 93.645 598 30 3 5498 6093 118646907 118647498 0.000000e+00 887.0
16 TraesCS7D01G199100 chr7B 90.611 671 43 15 4521 5177 118645831 118646495 0.000000e+00 872.0
17 TraesCS7D01G199100 chr7B 91.775 231 19 0 3545 3775 118644663 118644893 7.620000e-84 322.0
18 TraesCS7D01G199100 chr7B 88.073 109 9 2 5255 5363 118646591 118646695 6.410000e-25 126.0
19 TraesCS7D01G199100 chr1D 93.333 285 8 7 4967 5250 12785224 12785498 1.580000e-110 411.0
20 TraesCS7D01G199100 chr1D 92.857 266 18 1 5498 5763 12786011 12786275 9.580000e-103 385.0
21 TraesCS7D01G199100 chr1D 88.571 105 8 2 5259 5363 12785575 12785675 2.310000e-24 124.0
22 TraesCS7D01G199100 chr5D 92.857 266 18 1 5498 5763 438349697 438349433 9.580000e-103 385.0
23 TraesCS7D01G199100 chr5D 88.710 62 3 2 3774 3831 56125701 56125640 8.470000e-09 73.1
24 TraesCS7D01G199100 chr5D 87.931 58 5 2 3786 3841 69354216 69354273 3.940000e-07 67.6
25 TraesCS7D01G199100 chr5D 95.122 41 2 0 3792 3832 381914448 381914488 1.420000e-06 65.8
26 TraesCS7D01G199100 chr2A 92.395 263 19 1 5501 5763 274083808 274083547 2.070000e-99 374.0
27 TraesCS7D01G199100 chr2A 93.182 44 3 0 3793 3836 733925466 733925423 1.420000e-06 65.8
28 TraesCS7D01G199100 chr2D 87.218 266 18 6 5498 5763 29241636 29241885 7.730000e-74 289.0
29 TraesCS7D01G199100 chr6A 76.427 403 92 2 3999 4398 547812380 547812782 1.330000e-51 215.0
30 TraesCS7D01G199100 chr6A 89.091 55 3 2 3792 3844 586040336 586040389 1.420000e-06 65.8
31 TraesCS7D01G199100 chr6B 76.179 403 93 2 3999 4398 601344524 601344926 6.190000e-50 209.0
32 TraesCS7D01G199100 chr6D 75.743 404 93 4 3999 4398 401199554 401199956 1.340000e-46 198.0
33 TraesCS7D01G199100 chr4B 95.349 43 2 0 3790 3832 70256674 70256632 1.100000e-07 69.4
34 TraesCS7D01G199100 chr2B 89.091 55 2 2 3774 3824 587169324 587169378 1.420000e-06 65.8


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 TraesCS7D01G199100 chr7D 156213938 156220030 6092 False 2764.450000 10447 99.000000 1 6093 4 chr7D.!!$F1 6092
1 TraesCS7D01G199100 chr7D 351293464 351294515 1051 False 296.333333 385 90.908333 4967 5763 3 chr7D.!!$F2 796
2 TraesCS7D01G199100 chr7A 210849575 210856321 6746 False 1624.000000 3679 91.788000 3 6093 5 chr7A.!!$F2 6090
3 TraesCS7D01G199100 chr7B 118642068 118647498 5430 False 1106.666667 3406 91.854500 924 6093 6 chr7B.!!$F1 5169
4 TraesCS7D01G199100 chr1D 12785224 12786275 1051 False 306.666667 411 91.587000 4967 5763 3 chr1D.!!$F1 796

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
565 567 0.667487 TGAAGACTCGAAGGCAAGCG 60.667 55.0 0.00 0.0 0.00 4.68 F
704 706 0.696501 ACGCCACCTTGGTATTTCCT 59.303 50.0 0.00 0.0 40.46 3.36 F
2397 2452 0.820871 GTGAGACACTAGGCAGGAGG 59.179 60.0 0.00 0.0 0.00 4.30 F
3211 3684 0.594796 GGGTTTGTGCAAGTGCTTCG 60.595 55.0 4.69 0.0 42.66 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 2106 0.537188 GGAGGAAGCAGATCCACGAA 59.463 55.0 6.07 0.0 42.27 3.85 R
2674 2730 0.620700 AGGGCTGGTCCTTCGGTTAT 60.621 55.0 0.00 0.0 32.13 1.89 R
3216 3689 0.905337 AGATGTATCCGCCTAGCCCC 60.905 60.0 0.00 0.0 0.00 5.80 R
5179 5960 0.181114 AACCAAGAGACAGCAGCACA 59.819 50.0 0.00 0.0 0.00 4.57 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
49 50 2.793232 GACACGCACGAAAGAAACTACT 59.207 45.455 0.00 0.00 0.00 2.57
62 63 5.121380 AGAAACTACTCATGCATCCCAAT 57.879 39.130 0.00 0.00 0.00 3.16
76 77 6.028131 TGCATCCCAATCTATCTCCTATCTT 58.972 40.000 0.00 0.00 0.00 2.40
81 82 5.660864 CCCAATCTATCTCCTATCTTCCTCC 59.339 48.000 0.00 0.00 0.00 4.30
97 98 4.778415 CCGAGGCACTGGACGACG 62.778 72.222 0.00 0.00 41.55 5.12
113 114 2.307137 GACGTCGGCGGTGACTCTAG 62.307 65.000 16.39 0.00 43.45 2.43
134 135 5.789643 AGGTCACAGCAACAACAATAAAT 57.210 34.783 0.00 0.00 0.00 1.40
141 142 4.510711 CAGCAACAACAATAAATTGCCACA 59.489 37.500 4.29 0.00 46.89 4.17
156 157 1.376609 CCACACAATCTAAGCCGCCC 61.377 60.000 0.00 0.00 0.00 6.13
179 180 1.377202 GCAGTGGCGGATTCAGGAA 60.377 57.895 0.00 0.00 0.00 3.36
188 189 2.843701 CGGATTCAGGAAGATGAAGGG 58.156 52.381 0.00 0.00 42.20 3.95
225 226 8.713271 GTCAAACAATACTTGTAAGAAGAGAGG 58.287 37.037 0.00 0.00 44.59 3.69
230 231 4.706842 ACTTGTAAGAAGAGAGGCCAAA 57.293 40.909 5.01 0.00 0.00 3.28
485 486 3.292460 CCTAGAGGTAGAGTGTTGAGGG 58.708 54.545 0.00 0.00 0.00 4.30
498 499 2.306847 GTTGAGGGAAAAGCAAGGTGA 58.693 47.619 0.00 0.00 0.00 4.02
504 505 3.966665 AGGGAAAAGCAAGGTGAAAATCA 59.033 39.130 0.00 0.00 0.00 2.57
562 564 3.616956 ATCATGAAGACTCGAAGGCAA 57.383 42.857 0.00 0.00 0.00 4.52
563 565 2.964740 TCATGAAGACTCGAAGGCAAG 58.035 47.619 0.00 0.00 0.00 4.01
565 567 0.667487 TGAAGACTCGAAGGCAAGCG 60.667 55.000 0.00 0.00 0.00 4.68
566 568 1.355066 GAAGACTCGAAGGCAAGCGG 61.355 60.000 0.00 0.00 0.00 5.52
571 573 2.511600 CGAAGGCAAGCGGGTAGG 60.512 66.667 0.00 0.00 0.00 3.18
587 589 2.895404 GGTAGGAATACACCCGCTATCA 59.105 50.000 0.00 0.00 0.00 2.15
600 602 3.006859 CCCGCTATCAGTTGATCATGGTA 59.993 47.826 0.00 0.00 36.05 3.25
605 607 6.292542 CGCTATCAGTTGATCATGGTAACTTG 60.293 42.308 0.00 0.00 42.84 3.16
633 635 1.296715 CGGGGAGAAAGACACCAGG 59.703 63.158 0.00 0.00 0.00 4.45
650 652 2.478033 GGGGCGCCCTCATTTTACG 61.478 63.158 42.70 0.00 41.34 3.18
658 660 2.423538 GCCCTCATTTTACGACATTGCT 59.576 45.455 0.00 0.00 0.00 3.91
661 663 4.155826 CCCTCATTTTACGACATTGCTTCA 59.844 41.667 0.00 0.00 0.00 3.02
667 669 1.865865 ACGACATTGCTTCAGTTCGT 58.134 45.000 0.00 0.00 0.00 3.85
677 679 3.857665 TGCTTCAGTTCGTCGATATGTTC 59.142 43.478 0.00 0.00 0.00 3.18
687 689 7.375280 AGTTCGTCGATATGTTCTACAATTACG 59.625 37.037 0.00 0.00 0.00 3.18
704 706 0.696501 ACGCCACCTTGGTATTTCCT 59.303 50.000 0.00 0.00 40.46 3.36
714 716 4.505742 CCTTGGTATTTCCTCAGATAGCCC 60.506 50.000 0.00 0.00 37.07 5.19
721 723 5.912149 TTTCCTCAGATAGCCCATATGTT 57.088 39.130 1.24 0.00 0.00 2.71
722 724 7.574021 ATTTCCTCAGATAGCCCATATGTTA 57.426 36.000 1.24 0.00 0.00 2.41
732 734 5.693769 AGCCCATATGTTACTACACTTGT 57.306 39.130 1.24 0.00 37.03 3.16
737 739 7.625606 GCCCATATGTTACTACACTTGTTTGTC 60.626 40.741 1.24 0.00 37.03 3.18
742 744 6.636705 TGTTACTACACTTGTTTGTCTGAGT 58.363 36.000 0.00 0.00 0.00 3.41
746 748 7.772332 ACTACACTTGTTTGTCTGAGTTAAG 57.228 36.000 0.00 0.00 0.00 1.85
756 758 8.721478 TGTTTGTCTGAGTTAAGAGAAATATGC 58.279 33.333 0.65 0.00 40.36 3.14
816 823 6.540438 AACGAAATAAGTGGTCTCCTATGA 57.460 37.500 0.00 0.00 0.00 2.15
825 832 5.941788 AGTGGTCTCCTATGAACAAAAACT 58.058 37.500 0.00 0.00 35.23 2.66
863 870 1.133792 ACCAGAGACACCAACCAAAGG 60.134 52.381 0.00 0.00 0.00 3.11
906 913 0.872388 GAAAACACCACCTAGCACCG 59.128 55.000 0.00 0.00 0.00 4.94
925 932 3.505680 ACCGCAAGATGCAAAGATACAAA 59.494 39.130 2.99 0.00 45.36 2.83
926 933 4.158394 ACCGCAAGATGCAAAGATACAAAT 59.842 37.500 2.99 0.00 45.36 2.32
1076 1096 2.618312 ATTAGTACCCGCGACGCCAC 62.618 60.000 15.34 7.30 0.00 5.01
1234 1261 1.078848 CACAGTAGGCAGGTGAGGC 60.079 63.158 0.00 0.00 34.52 4.70
2040 2067 1.403814 TCGAGGCCAAGAGATTCGAT 58.596 50.000 5.01 0.00 35.60 3.59
2079 2106 2.370349 ACCATCGTCGAGATCTTCTGT 58.630 47.619 0.00 0.00 37.52 3.41
2095 2122 1.066858 TCTGTTCGTGGATCTGCTTCC 60.067 52.381 0.00 0.00 36.24 3.46
2180 2207 1.441729 GGATGATCGAGGCGTGGAA 59.558 57.895 0.00 0.00 0.00 3.53
2280 2332 4.601019 GTGATGTCACCAGTGTTCTTTTG 58.399 43.478 1.68 0.00 40.85 2.44
2281 2333 3.631686 TGATGTCACCAGTGTTCTTTTGG 59.368 43.478 0.00 0.00 37.98 3.28
2397 2452 0.820871 GTGAGACACTAGGCAGGAGG 59.179 60.000 0.00 0.00 0.00 4.30
2450 2505 8.837788 AGAGGAAATTCAAAAATGTTCCATTC 57.162 30.769 3.76 0.00 36.06 2.67
2526 2582 1.503347 ACTCCAATTGGGTTTCCTGGT 59.497 47.619 24.29 7.77 38.11 4.00
2646 2702 4.516698 CAGTTACAAAGAGGAACATGCTGT 59.483 41.667 0.00 0.00 0.00 4.40
2674 2730 2.028484 GTCACCGCCGTCAGTCAA 59.972 61.111 0.00 0.00 0.00 3.18
2727 2783 2.914777 GAAGAGCTCGCCGCCTTCAT 62.915 60.000 8.37 0.00 41.53 2.57
2777 2839 2.915738 ATGACTACAAGGTCGACGTC 57.084 50.000 11.73 11.20 38.91 4.34
2782 2844 2.462255 TACAAGGTCGACGTCACCGC 62.462 60.000 22.85 8.66 39.13 5.68
2939 3001 1.133407 CGCAAGTCAGGGTCTAGAGTC 59.867 57.143 0.00 0.00 0.00 3.36
2965 3030 1.802365 GTTTAACGGCGATGGTGACTT 59.198 47.619 16.62 0.00 0.00 3.01
2972 3037 1.610624 GGCGATGGTGACTTGGAAGAA 60.611 52.381 0.00 0.00 0.00 2.52
3147 3212 8.792830 TCTCCAGGTAAATTTCTCTTGTTATG 57.207 34.615 0.00 0.00 0.00 1.90
3184 3657 5.932303 TCTTTAGAACCCGATGAAACTCTTG 59.068 40.000 0.00 0.00 0.00 3.02
3194 3667 6.460123 CCCGATGAAACTCTTGATTATTTGGG 60.460 42.308 0.00 0.00 0.00 4.12
3211 3684 0.594796 GGGTTTGTGCAAGTGCTTCG 60.595 55.000 4.69 0.00 42.66 3.79
3215 3688 1.522668 TTGTGCAAGTGCTTCGCTAT 58.477 45.000 4.69 0.00 42.66 2.97
3216 3689 0.798159 TGTGCAAGTGCTTCGCTATG 59.202 50.000 4.69 0.00 42.66 2.23
3225 3698 1.004440 CTTCGCTATGGGGCTAGGC 60.004 63.158 8.00 8.00 0.00 3.93
3503 3981 9.424319 GAAGAGTTGATTGTATACTTCTGAACA 57.576 33.333 4.17 0.00 32.46 3.18
3606 4115 2.658285 ACGAACCATGCATCCATTCAT 58.342 42.857 0.00 0.00 0.00 2.57
3895 4425 7.252708 CAATGTATAGAGCAGCATGTTTTTCA 58.747 34.615 0.00 0.00 39.31 2.69
3901 4431 6.374565 AGAGCAGCATGTTTTTCAGATATC 57.625 37.500 0.00 0.00 39.31 1.63
3902 4432 5.884232 AGAGCAGCATGTTTTTCAGATATCA 59.116 36.000 5.32 0.00 39.31 2.15
3922 4452 5.173774 TCATATCTTTTGCTGCCGATTTC 57.826 39.130 0.00 0.00 0.00 2.17
3969 4512 2.629137 TGTGTCCATGCTTGCTGAAAAT 59.371 40.909 0.00 0.00 0.00 1.82
4255 4962 0.381801 CGAGGAGAGCAGAGCTTCTC 59.618 60.000 4.79 4.79 39.88 2.87
4256 4963 1.473258 GAGGAGAGCAGAGCTTCTCA 58.527 55.000 13.73 0.00 39.88 3.27
4293 5000 1.518367 AGTTTGGAGTTCAGGGTGGA 58.482 50.000 0.00 0.00 0.00 4.02
4319 5026 0.698238 ACCAACCCATTAGCAGAGCA 59.302 50.000 0.00 0.00 0.00 4.26
4320 5027 1.340405 ACCAACCCATTAGCAGAGCAG 60.340 52.381 0.00 0.00 0.00 4.24
4335 5042 3.366121 CAGAGCAGAACACTTCATACGTG 59.634 47.826 0.00 0.00 38.32 4.49
4426 5133 2.540973 CGATCGACGCTAATTCACCTCA 60.541 50.000 10.26 0.00 34.51 3.86
4570 5282 5.543714 TGCAATGCATCTTCACAGAATTTT 58.456 33.333 2.72 0.00 31.71 1.82
4655 5427 1.564348 TCCTTTCTTATCCAGCCACCC 59.436 52.381 0.00 0.00 0.00 4.61
4656 5428 1.284785 CCTTTCTTATCCAGCCACCCA 59.715 52.381 0.00 0.00 0.00 4.51
4658 5430 0.918983 TTCTTATCCAGCCACCCAGG 59.081 55.000 0.00 0.00 41.84 4.45
4677 5449 5.244626 CCCAGGAATTGATGTATTTCCATCC 59.755 44.000 3.96 0.00 40.43 3.51
4688 5460 6.528537 TGTATTTCCATCCTGTCCATTTTG 57.471 37.500 0.00 0.00 0.00 2.44
4695 5467 0.604578 CCTGTCCATTTTGTGCAGGG 59.395 55.000 0.00 0.00 42.05 4.45
4696 5468 0.604578 CTGTCCATTTTGTGCAGGGG 59.395 55.000 0.00 0.00 0.00 4.79
4734 5508 1.562942 TGCTCCATCTGAAGCCTGAAT 59.437 47.619 0.00 0.00 0.00 2.57
4744 5518 1.404391 GAAGCCTGAATCACCTGCATG 59.596 52.381 0.00 0.00 0.00 4.06
4878 5653 1.492319 TTTGCGAGTTGGTTCGACGG 61.492 55.000 0.00 0.00 43.03 4.79
4893 5668 1.710013 GACGGTTCAGATTTCTGCGA 58.290 50.000 11.35 0.00 43.46 5.10
5000 5778 2.596851 GCCCCTGCAGGTCTTGAGA 61.597 63.158 30.63 0.00 37.47 3.27
5067 5847 2.055100 GTTCCTATCTTCGCGAGATGC 58.945 52.381 22.87 5.96 44.80 3.91
5222 6004 2.031682 GCTTGTTTGAGTGTGGCTACTG 60.032 50.000 0.64 0.00 0.00 2.74
5276 6127 2.702751 ATCGTGTTGCCGGACGAACA 62.703 55.000 18.48 13.76 46.83 3.18
5283 6134 2.182030 CCGGACGAACAGAGCCTC 59.818 66.667 0.00 0.00 0.00 4.70
5294 6145 2.532843 ACAGAGCCTCCATTTTGCATT 58.467 42.857 0.00 0.00 0.00 3.56
5296 6147 1.206371 AGAGCCTCCATTTTGCATTGC 59.794 47.619 0.46 0.46 0.00 3.56
5299 6150 0.108520 CCTCCATTTTGCATTGCGCT 60.109 50.000 9.73 0.00 43.06 5.92
5304 6155 1.652124 CATTTTGCATTGCGCTCACTC 59.348 47.619 9.73 0.00 43.06 3.51
5396 6469 3.963383 ACTTGTAAAAGCTGACCAACG 57.037 42.857 0.00 0.00 0.00 4.10
5452 6532 6.543465 CCTGATAATGTTTTCCAGCATACAGA 59.457 38.462 0.00 0.00 0.00 3.41
5458 6538 1.448985 TTCCAGCATACAGAAACGCC 58.551 50.000 0.00 0.00 0.00 5.68
5466 6546 1.053424 TACAGAAACGCCAGGGAAGT 58.947 50.000 0.00 0.00 0.00 3.01
5481 6561 6.472887 CCAGGGAAGTAACAGATCTACAAAA 58.527 40.000 0.00 0.00 0.00 2.44
5496 6576 6.453926 TCTACAAAACCTAAAACACAACCC 57.546 37.500 0.00 0.00 0.00 4.11
5499 6653 1.765230 AACCTAAAACACAACCCGCA 58.235 45.000 0.00 0.00 0.00 5.69
5504 6658 1.846541 AAAACACAACCCGCATTTCG 58.153 45.000 0.00 0.00 38.08 3.46
5523 6677 4.214986 TCGGCCATCTTCAGAAAATGTA 57.785 40.909 2.24 0.00 0.00 2.29
5524 6678 4.780815 TCGGCCATCTTCAGAAAATGTAT 58.219 39.130 2.24 0.00 0.00 2.29
5552 6706 5.615495 CAGAATTTGCATATGTGAAAGCG 57.385 39.130 4.29 0.00 0.00 4.68
5575 6729 8.097038 AGCGGTCATATAACAAGAATCATGTAT 58.903 33.333 0.00 0.00 0.00 2.29
5631 6785 2.288579 TGATGTCGCTACAAAACTCGGT 60.289 45.455 0.00 0.00 39.58 4.69
5730 6884 1.273455 CTGTGAGCGCAAAAAGCTGC 61.273 55.000 11.47 0.00 46.13 5.25
5790 6944 2.280628 CTCCAATAACCTGCTCCGAAC 58.719 52.381 0.00 0.00 0.00 3.95
5873 7027 3.588955 CTTGCAGGTAAAATGAAAGGCC 58.411 45.455 0.00 0.00 30.72 5.19
5891 7047 1.129811 GCCGGTCAAATAACTGAACCG 59.870 52.381 1.90 5.31 38.56 4.44
5916 7072 0.108233 CTCAGGCTGCTCAGAGGAAC 60.108 60.000 10.34 0.00 0.00 3.62
5917 7073 0.833409 TCAGGCTGCTCAGAGGAACA 60.833 55.000 10.34 0.00 0.00 3.18
5930 7086 3.304559 CAGAGGAACATTTCGACGATCAC 59.695 47.826 0.00 0.00 0.00 3.06
5931 7087 3.056821 AGAGGAACATTTCGACGATCACA 60.057 43.478 0.00 0.00 0.00 3.58
5976 7132 3.317149 ACCAGATGAACACATATGCATGC 59.683 43.478 11.82 11.82 35.39 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.593128 ATGGTGTGTCGCTTTTCTGC 59.407 50.000 0.00 0.00 0.00 4.26
3 4 2.033299 ACAATGGTGTGTCGCTTTTCTG 59.967 45.455 0.00 0.00 36.31 3.02
5 6 2.774439 ACAATGGTGTGTCGCTTTTC 57.226 45.000 0.00 0.00 36.31 2.29
14 15 0.657077 CGTGTCGCAACAATGGTGTG 60.657 55.000 5.32 5.32 38.27 3.82
36 37 4.034510 GGGATGCATGAGTAGTTTCTTTCG 59.965 45.833 2.46 0.00 0.00 3.46
49 50 4.173594 AGGAGATAGATTGGGATGCATGA 58.826 43.478 2.46 0.00 0.00 3.07
62 63 4.226394 CCTCGGAGGAAGATAGGAGATAGA 59.774 50.000 19.57 0.00 37.67 1.98
76 77 2.680352 GTCCAGTGCCTCGGAGGA 60.680 66.667 27.95 9.96 37.67 3.71
81 82 3.948086 GACGTCGTCCAGTGCCTCG 62.948 68.421 14.60 0.00 0.00 4.63
97 98 1.991099 GACCTAGAGTCACCGCCGAC 61.991 65.000 0.00 0.00 45.55 4.79
113 114 5.333263 GCAATTTATTGTTGTTGCTGTGACC 60.333 40.000 4.54 0.00 42.61 4.02
118 119 4.510711 TGTGGCAATTTATTGTTGTTGCTG 59.489 37.500 8.57 0.00 44.64 4.41
134 135 1.164411 CGGCTTAGATTGTGTGGCAA 58.836 50.000 0.00 0.00 41.89 4.52
141 142 0.394352 CCTTGGGCGGCTTAGATTGT 60.394 55.000 9.56 0.00 0.00 2.71
156 157 2.361610 AATCCGCCACTGCCCTTG 60.362 61.111 0.00 0.00 0.00 3.61
166 167 2.216898 CTTCATCTTCCTGAATCCGCC 58.783 52.381 0.00 0.00 34.76 6.13
179 180 4.043310 TGACTCATTTGGTTCCCTTCATCT 59.957 41.667 0.00 0.00 0.00 2.90
188 189 8.285776 CAAGTATTGTTTGACTCATTTGGTTC 57.714 34.615 0.00 0.00 42.34 3.62
498 499 4.262420 CCCACAATCTTTTCCGGTGATTTT 60.262 41.667 0.00 0.00 0.00 1.82
504 505 0.774908 TCCCCACAATCTTTTCCGGT 59.225 50.000 0.00 0.00 0.00 5.28
562 564 2.524611 GGGTGTATTCCTACCCGCT 58.475 57.895 0.00 0.00 46.42 5.52
566 568 2.895404 TGATAGCGGGTGTATTCCTACC 59.105 50.000 0.00 0.00 36.21 3.18
571 573 4.054780 TCAACTGATAGCGGGTGTATTC 57.945 45.455 4.48 0.00 39.22 1.75
580 582 5.292765 AGTTACCATGATCAACTGATAGCG 58.707 41.667 0.00 0.00 34.37 4.26
587 589 4.702131 GCCTTCAAGTTACCATGATCAACT 59.298 41.667 0.00 0.00 34.03 3.16
600 602 2.978010 CCGCACGGCCTTCAAGTT 60.978 61.111 0.00 0.00 0.00 2.66
610 612 2.434359 GTCTTTCTCCCCGCACGG 60.434 66.667 1.02 1.02 0.00 4.94
619 621 1.376037 CGCCCCTGGTGTCTTTCTC 60.376 63.158 0.00 0.00 0.00 2.87
633 635 1.450669 TCGTAAAATGAGGGCGCCC 60.451 57.895 39.29 39.29 0.00 6.13
640 642 5.931532 ACTGAAGCAATGTCGTAAAATGAG 58.068 37.500 0.00 0.00 0.00 2.90
646 648 3.386486 ACGAACTGAAGCAATGTCGTAA 58.614 40.909 0.00 0.00 0.00 3.18
650 652 2.058798 TCGACGAACTGAAGCAATGTC 58.941 47.619 0.00 0.00 0.00 3.06
658 660 6.185852 TGTAGAACATATCGACGAACTGAA 57.814 37.500 14.67 0.00 36.54 3.02
661 663 7.375280 CGTAATTGTAGAACATATCGACGAACT 59.625 37.037 0.00 0.00 36.54 3.01
667 669 5.688621 GTGGCGTAATTGTAGAACATATCGA 59.311 40.000 0.00 0.00 0.00 3.59
677 679 2.706890 ACCAAGGTGGCGTAATTGTAG 58.293 47.619 0.00 0.00 42.67 2.74
687 689 2.026262 TCTGAGGAAATACCAAGGTGGC 60.026 50.000 1.07 0.00 42.67 5.01
704 706 7.010771 AGTGTAGTAACATATGGGCTATCTGA 58.989 38.462 7.80 0.00 38.08 3.27
714 716 9.203421 TCAGACAAACAAGTGTAGTAACATATG 57.797 33.333 0.00 0.00 38.08 1.78
721 723 8.689061 TCTTAACTCAGACAAACAAGTGTAGTA 58.311 33.333 0.00 0.00 0.00 1.82
722 724 7.553334 TCTTAACTCAGACAAACAAGTGTAGT 58.447 34.615 0.00 0.00 0.00 2.73
816 823 4.869861 GCCAACAAGTGATGAGTTTTTGTT 59.130 37.500 0.00 0.00 41.23 2.83
825 832 0.953727 GTGCTGCCAACAAGTGATGA 59.046 50.000 0.00 0.00 0.00 2.92
1076 1096 2.534272 TTGGGTTGGGAGGGGAGG 60.534 66.667 0.00 0.00 0.00 4.30
1080 1100 3.992641 GGGGTTGGGTTGGGAGGG 61.993 72.222 0.00 0.00 0.00 4.30
1083 1103 3.253838 CGAGGGGTTGGGTTGGGA 61.254 66.667 0.00 0.00 0.00 4.37
1178 1204 3.215245 CTCGCAAGGAGGAGGGAG 58.785 66.667 0.00 0.00 39.22 4.30
1216 1243 1.078848 GCCTCACCTGCCTACTGTG 60.079 63.158 0.00 0.00 0.00 3.66
1746 1773 1.451747 GAGGTAGTCGGCGAGGTCT 60.452 63.158 11.20 6.82 0.00 3.85
2040 2067 1.925285 TAGACGAGGGGCCGACCTTA 61.925 60.000 1.63 0.00 42.10 2.69
2079 2106 0.537188 GGAGGAAGCAGATCCACGAA 59.463 55.000 6.07 0.00 42.27 3.85
2095 2122 4.583871 AGCCTAGAAATGTCAACAAGGAG 58.416 43.478 2.67 0.00 0.00 3.69
2371 2426 2.171659 TGCCTAGTGTCTCACCAAAACA 59.828 45.455 0.00 0.00 34.49 2.83
2397 2452 7.921745 GTCATATAGTACCAGGAAAGAACAGTC 59.078 40.741 0.00 0.00 0.00 3.51
2478 2533 9.942850 TGCATATGTAATAGTAGTACAATGCAT 57.057 29.630 30.34 15.60 42.63 3.96
2479 2534 9.942850 ATGCATATGTAATAGTAGTACAATGCA 57.057 29.630 32.66 32.66 45.94 3.96
2646 2702 4.680237 CGGTGACCTGCTTGCCGA 62.680 66.667 0.00 0.00 44.57 5.54
2674 2730 0.620700 AGGGCTGGTCCTTCGGTTAT 60.621 55.000 0.00 0.00 32.13 1.89
2954 3019 2.160417 GCTTTCTTCCAAGTCACCATCG 59.840 50.000 0.00 0.00 0.00 3.84
2965 3030 0.472471 AACCTCGGTGCTTTCTTCCA 59.528 50.000 0.00 0.00 0.00 3.53
2972 3037 0.036010 CATCCTCAACCTCGGTGCTT 60.036 55.000 0.00 0.00 0.00 3.91
3147 3212 6.697892 CGGGTTCTAAAGAGATGACATAGAAC 59.302 42.308 14.27 14.27 45.88 3.01
3184 3657 4.152223 GCACTTGCACAAACCCAAATAATC 59.848 41.667 0.00 0.00 41.59 1.75
3211 3684 0.976073 TATCCGCCTAGCCCCATAGC 60.976 60.000 0.00 0.00 0.00 2.97
3215 3688 1.152118 ATGTATCCGCCTAGCCCCA 60.152 57.895 0.00 0.00 0.00 4.96
3216 3689 0.905337 AGATGTATCCGCCTAGCCCC 60.905 60.000 0.00 0.00 0.00 5.80
3225 3698 2.544694 GCAGACACTGGAGATGTATCCG 60.545 54.545 0.00 0.00 42.77 4.18
3322 3796 5.888161 AGAAATTTAGTGGGCTAAGATGGTG 59.112 40.000 0.00 0.00 38.31 4.17
3503 3981 4.746466 TGAGTTCCCCCAATGTTTATGTT 58.254 39.130 0.00 0.00 0.00 2.71
3606 4115 3.146066 GGTTAGTGCCATCAAGACACAA 58.854 45.455 0.00 0.00 36.76 3.33
3895 4425 5.798132 TCGGCAGCAAAAGATATGATATCT 58.202 37.500 9.11 9.11 0.00 1.98
3901 4431 5.179045 AGAAATCGGCAGCAAAAGATATG 57.821 39.130 0.00 0.00 0.00 1.78
3902 4432 6.150140 GGATAGAAATCGGCAGCAAAAGATAT 59.850 38.462 0.00 0.00 32.44 1.63
3922 4452 8.192774 AGTGTACATTTGCAAAATGATGGATAG 58.807 33.333 17.19 0.00 0.00 2.08
4255 4962 2.503356 ACTTCTGCCTCTCCCACTTATG 59.497 50.000 0.00 0.00 0.00 1.90
4256 4963 2.839228 ACTTCTGCCTCTCCCACTTAT 58.161 47.619 0.00 0.00 0.00 1.73
4319 5026 3.367498 GCTCCTCACGTATGAAGTGTTCT 60.367 47.826 0.00 0.00 40.28 3.01
4320 5027 2.924290 GCTCCTCACGTATGAAGTGTTC 59.076 50.000 0.00 0.00 40.28 3.18
4335 5042 2.946762 GCAACCAACGTGCTCCTC 59.053 61.111 0.00 0.00 39.00 3.71
4677 5449 0.604578 CCCCTGCACAAAATGGACAG 59.395 55.000 0.00 0.00 0.00 3.51
4695 5467 3.810896 CTTTGCCGCCTAACGCCC 61.811 66.667 0.00 0.00 41.76 6.13
4696 5468 2.112815 ATCTTTGCCGCCTAACGCC 61.113 57.895 0.00 0.00 41.76 5.68
4734 5508 1.218047 GCCTCGTACATGCAGGTGA 59.782 57.895 15.48 2.52 0.00 4.02
4765 5539 3.822167 TGTGATGAAGTGACATGTTGCAT 59.178 39.130 0.00 0.00 0.00 3.96
4768 5542 6.250344 AGAATGTGATGAAGTGACATGTTG 57.750 37.500 0.00 0.00 34.72 3.33
4893 5668 3.558109 GCTTTAGAGTCCAGGCTCTGTTT 60.558 47.826 18.67 1.34 44.71 2.83
5162 5943 5.528690 GCAGCACATATAACAGATGAAGGAA 59.471 40.000 0.00 0.00 0.00 3.36
5164 5945 5.049612 CAGCAGCACATATAACAGATGAAGG 60.050 44.000 0.00 0.00 0.00 3.46
5165 5946 5.526479 ACAGCAGCACATATAACAGATGAAG 59.474 40.000 0.00 0.00 0.00 3.02
5167 5948 5.027293 ACAGCAGCACATATAACAGATGA 57.973 39.130 0.00 0.00 0.00 2.92
5168 5949 5.055144 AGACAGCAGCACATATAACAGATG 58.945 41.667 0.00 0.00 0.00 2.90
5169 5950 5.070180 AGAGACAGCAGCACATATAACAGAT 59.930 40.000 0.00 0.00 0.00 2.90
5171 5952 4.691175 AGAGACAGCAGCACATATAACAG 58.309 43.478 0.00 0.00 0.00 3.16
5173 5954 4.272018 CCAAGAGACAGCAGCACATATAAC 59.728 45.833 0.00 0.00 0.00 1.89
5174 5955 4.080919 ACCAAGAGACAGCAGCACATATAA 60.081 41.667 0.00 0.00 0.00 0.98
5175 5956 3.452264 ACCAAGAGACAGCAGCACATATA 59.548 43.478 0.00 0.00 0.00 0.86
5176 5957 2.238144 ACCAAGAGACAGCAGCACATAT 59.762 45.455 0.00 0.00 0.00 1.78
5177 5958 1.625315 ACCAAGAGACAGCAGCACATA 59.375 47.619 0.00 0.00 0.00 2.29
5178 5959 0.399454 ACCAAGAGACAGCAGCACAT 59.601 50.000 0.00 0.00 0.00 3.21
5179 5960 0.181114 AACCAAGAGACAGCAGCACA 59.819 50.000 0.00 0.00 0.00 4.57
5180 5961 0.871057 GAACCAAGAGACAGCAGCAC 59.129 55.000 0.00 0.00 0.00 4.40
5250 6033 1.012343 CGGCAACACGATGTATGCG 60.012 57.895 0.00 0.00 36.20 4.73
5252 6035 0.650512 GTCCGGCAACACGATGTATG 59.349 55.000 0.00 0.00 35.47 2.39
5253 6036 0.804544 CGTCCGGCAACACGATGTAT 60.805 55.000 7.60 0.00 38.16 2.29
5276 6127 1.206371 GCAATGCAAAATGGAGGCTCT 59.794 47.619 15.23 0.00 0.00 4.09
5294 6145 2.455674 ATTACAAGTGAGTGAGCGCA 57.544 45.000 11.47 0.00 0.00 6.09
5296 6147 4.213270 TCCAAAATTACAAGTGAGTGAGCG 59.787 41.667 0.00 0.00 0.00 5.03
5299 6150 5.534278 TGCATCCAAAATTACAAGTGAGTGA 59.466 36.000 0.00 0.00 0.00 3.41
5304 6155 6.841443 TTGTTGCATCCAAAATTACAAGTG 57.159 33.333 0.00 0.00 31.68 3.16
5370 6443 7.434013 CGTTGGTCAGCTTTTACAAGTTTTATT 59.566 33.333 0.00 0.00 31.86 1.40
5379 6452 0.948678 GCCGTTGGTCAGCTTTTACA 59.051 50.000 0.00 0.00 0.00 2.41
5380 6453 0.948678 TGCCGTTGGTCAGCTTTTAC 59.051 50.000 0.00 0.00 0.00 2.01
5396 6469 0.525761 TTTTATTGCCGAGCAGTGCC 59.474 50.000 12.58 2.23 40.61 5.01
5452 6532 1.418637 TCTGTTACTTCCCTGGCGTTT 59.581 47.619 0.00 0.00 0.00 3.60
5458 6538 6.371825 GGTTTTGTAGATCTGTTACTTCCCTG 59.628 42.308 5.18 0.00 0.00 4.45
5466 6546 9.616156 TGTGTTTTAGGTTTTGTAGATCTGTTA 57.384 29.630 5.18 0.00 0.00 2.41
5481 6561 1.989706 ATGCGGGTTGTGTTTTAGGT 58.010 45.000 0.00 0.00 0.00 3.08
5496 6576 0.028505 CTGAAGATGGCCGAAATGCG 59.971 55.000 0.00 0.00 40.47 4.73
5499 6653 4.463891 ACATTTTCTGAAGATGGCCGAAAT 59.536 37.500 20.76 0.30 0.00 2.17
5504 6658 6.016777 CCTGTATACATTTTCTGAAGATGGCC 60.017 42.308 20.76 0.00 0.00 5.36
5511 6665 8.579850 AATTCTGCCTGTATACATTTTCTGAA 57.420 30.769 5.91 10.88 0.00 3.02
5575 6729 7.178451 TGTGGACAATATCTGAGACAGTTTAGA 59.822 37.037 0.00 0.00 32.61 2.10
5592 6746 3.576078 TCACAGAACCTTGTGGACAAT 57.424 42.857 6.33 0.00 46.55 2.71
5730 6884 2.673368 GCTGTCACCTCCACTTTTATCG 59.327 50.000 0.00 0.00 0.00 2.92
5790 6944 3.062042 GCAAATTGGAAGTTTGAGGCAG 58.938 45.455 3.03 0.00 38.51 4.85
5861 7015 5.011635 AGTTATTTGACCGGCCTTTCATTTT 59.988 36.000 0.00 0.00 0.00 1.82
5873 7027 1.801771 TGCGGTTCAGTTATTTGACCG 59.198 47.619 8.72 8.72 40.97 4.79
5891 7047 0.733729 CTGAGCAGCCTGAGAATTGC 59.266 55.000 0.00 0.00 36.83 3.56
5916 7072 5.200454 GGATTGAATGTGATCGTCGAAATG 58.800 41.667 0.00 0.00 0.00 2.32
5917 7073 4.273480 GGGATTGAATGTGATCGTCGAAAT 59.727 41.667 0.00 0.00 0.00 2.17
5930 7086 5.430886 TGACATACAGTGAGGGATTGAATG 58.569 41.667 0.00 0.00 0.00 2.67
5931 7087 5.698741 TGACATACAGTGAGGGATTGAAT 57.301 39.130 0.00 0.00 0.00 2.57
5976 7132 0.671781 CTGGAACACCTGCTCTTCCG 60.672 60.000 0.00 0.00 36.94 4.30


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

AutoCloner maintained by Alex Coulton.